2024-03-28T21:15:52Zhttp://oai-repositori.upf.edu/oai/requestoai:repositori.upf.edu:10230/246452018-02-19T12:31:38Zcom_10230_5963col_10230_24644
Radó i Trilla, Núria, 1985-
2015-07-24T12:07:35Z
2015-07-24T12:07:35Z
2013
http://hdl.handle.net/10230/24645
Capítol 1: Adaptive evolution of orthologs: role of low-complexity regions: Cap1_SupMat: Document amb el material suplementari d’aquest capítol; Cap1_Data: Excel amb totes les dades utilitzades per l’elaboració de l’article que forma aquest capítol. Capítol 2: LCRs as a mechanism of new coding sequences formation: Cap2_SupMat: Document amb el material suplementari d’aquest capítol; Cap2_Data: Excel amb totes les dades utilitzades per l’elaboració de l’article que forma aquest capítol. Capítol 3: LCRs as a mechanism of protein diversification: Cap3_Data: Excel amb tots els identificadors classificats utilitzats per l’elaboració del capítol; Cap3_Exp: Tots els resultats experimentals que se citen al capítol
Dades primàries de la tesi “Low-complexity regions as a source of evolutionary innovation”/nde Núria Radó-Trilla http://hdl.handle.net/10803/113603
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application/pdf
eng
http://hdl.handle.net/10803/113603
CC0 1.0 Universal
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
Low-complexity regions in proteins as a source of evolutionary innovation [research data]
info:eu-repo/semantics/other
Dataset
THUMBNAIL
NRADO_Cap1_SupMat.pdf.jpg
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10230/24645
oai:repositori.upf.edu:10230/24645
2018-02-19 13:31:38.684
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/256082016-01-20T17:02:31Zcom_10230_5963col_10230_24644
Cornes Maragliano, Eric, 1987-
2016-01-20T16:59:35Z
2016-01-20T16:59:35Z
2015
http://hdl.handle.net/10230/25608
Table S1. RNAi phenotypes of lsm genes retrieved from wormmart./nWormmart is a tool available at wormbase [S1]. RNAi assays represented in this table were performed following diverse protocols and using distinct genetic backgrounds: /nRNAi by feeding starting at L4 [S2], RNAi by feeding starting at L1 [S3], RNAi in RNAi hypersensitive backgrounds [S4, S5], RNAi by injection [S6], or RNAi by soaking [S7]. Other RNAi screens referred here were focused in specific phenotypes as aging, cell proliferation, endocytosis, innate immunity or transgene silencing [S8–13]./n/nTable S2. Yeast lsm phenome./nTable shows all the yeast lsm phenotypes retrieved from the Saccharomyces Genome Database (SGD) [S13]. All the information available for S. cerevisiae mutant strains for lsm genes is shown. Non-viable phenotypes are highlighted in red. /n/nTable S3. RNA-Seq analyses of lsm-1 mutants. /nSheet 1: Statistical analyses including FPKM (fragments per kilobase of exon per million fragments mapped) for each gene mapped, and fold change between lsm-1 mutants and wild type animals. /nSheet 2: Genes significantly upregulated (p value ≤ 0.05). /nSheet 3: Genes significantly downregulated (p value ≤ 0.05). /nSheets 4 and 5: Additional information about genes up and down regulated in lsm-1 mutants. Gene description was retrieved from wormbase using the tool wormmart.
Research data from the thesis “A functional study of the conserved LSM proteins in C. elegans reveals their involvement in the stress response of metazoans” by Eric Cornes http://hdl.handle.net/10803/315473
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eng
http://hdl.handle.net/10803/315473
CC0 1.0 Universal
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
A functional study of the conserved LSM proteins in C. elegans reveals their involvement in the stress response of metazoans [datasets]
info:eu-repo/semantics/other
ORIGINAL
Table S3.xlsx
Table S3.xlsx
RNA-Seq analyses of lsm-1 mutants
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RNAi phenotypes of lsm genes retrieved from wormmart
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Description Spanish and References.docx
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oai:repositori.upf.edu:10230/25608
2016-01-20 18:02:31.392
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/276362016-12-19T08:52:29Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstmann, Rodrigo
González-Pérez, Abel
López Bigas, Núria
2016-11-30T10:48:39Z
2016-11-30T10:48:39Z
2016-10-17
http://hdl.handle.net/10230/27636
1 TSV (tab-separated values) file
The cancer bioMarkers database is curated and maintained by several clinical and scientific experts in the field of precision oncology supported by the European Union’s Horizon 2020 funding. This database is currently being integrated with knowledge databases of other institutions in a collaborative effort of the Global Alliance for Genomics and Health.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2016-11-30T10:48:39Z/nNo. of bitstreams: 2/nbiomarkers.tsv.gz: 28795 bytes, checksum: 58aae50387f5b65dabfc2b9a93e0c8a3 (MD5)/nlicense_rdf: 1089 bytes, checksum: 0a703d871bf062c5fdc7850b1496693b (MD5)
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eng
Universitat Pompeu Fabra
Més informació: Cancer bioMarkers database (Cancer Genome Interpreter)
https://www.cancergenomeinterpreter.org/biomarkers
Creative Commons CC0
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
Cancer bioMarkers database
info:eu-repo/semantics/other
Dataset
Cancer biomarkers
Precision medicine
ORIGINAL
biomarkers.tsv
biomarkers.tsv
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10230/27636
oai:repositori.upf.edu:10230/27636
2016-12-19 09:52:29.931
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/277842017-02-27T11:44:32Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
López Bigas, Núria
González-Pérez, Abel
Rubio Pérez, Carlota
Déu Pons, Jordi
2016-12-16T12:31:28Z
2016-12-16T12:31:28Z
2016-10-16
http://hdl.handle.net/10230/27784
Software: Docker 1.12+.
A tool aimed at the rational design of cancer gene panels. It estimates the cost-effectiveness of the designed panel on a cohort of tumors and provides reports on the importance of individual mutations for tumorigenesis or therapy.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2016-12-16T12:31:28Z/nNo. of bitstreams: 1/nbbglab_oncopad_1.0.tar(37).xz: 470258952 bytes, checksum: 48ed5feaa9ab1bb0c3fa59d563564c9c (MD5)
Made available in DSpace on 2016-12-16T12:31:28Z (GMT). No. of bitstreams: 1/nbbglab_oncopad_1.0.tar(37).xz: 470258952 bytes, checksum: 48ed5feaa9ab1bb0c3fa59d563564c9c (MD5)/n Previous issue date: 2016-10-16
eng
Universitat Pompeu Fabra
Més informació: OncoPAD (Bitbucket)
Rubio-Perez C, Deu-Pons J, Tamborero D, Lopez-Bigas N, Gonzalez-Perez A. Rational design of cancer gene panels with OncoPaD. Genome Med. 2016; 8(98). DOI: 10.1186/s13073-016-0349-1 http://hdl.handle.net/10230/27942
http://hdl.handle.net/10230/27942
https://bitbucket.org/bbglab/oncopad
OncoPAD is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto. Copyright® 2012-2014 Universitat Pompeu Fabra.
OncoPAD is made available to the general public subject to certain conditions described in its license. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of IntOGen Mutations Analysis may be sent via e-mail to innovacio@upf.edu.
Third Party Software - Third Party Data
All rights in any third-party data and/or any third-party software, including all ownership rights, are reserved and remain with the respective third parties. You agree that these third parties may enforce their rights under this agreement against you directly in their own name.
http://bitbucket.org/bbglab/oncopad/raw/619011cedb025d4542b7abc54d41b69636264575/LICENSE
info:eu-repo/semantics/openAccess
Cancer gene panel
OncoPaD
info:eu-repo/semantics/other
ORIGINAL
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oai:repositori.upf.edu:10230/27784
2017-02-27 12:44:32.447
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/278102017-02-03T12:21:32Zcom_10230_5963col_10230_24644
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Jené i Sanz, Alba, 1984-
Santos, Alberto
López Bigas, Núria
Déu Pons, Jordi
2016-12-21T11:51:09Z
2016-12-21T11:51:09Z
2016-07-18
http://hdl.handle.net/10230/27810
Requirements: IntOGen depends on **Python 3.4** or above and some python libraries. If you don't have Python 3.4 already installed, the easiest way to install all this software stack is using the well known [Anaconda Python distribution](http://continuum.io/downloads#34). /nAlso **Perl 5.10** (with DBI module installed) or above has to be available at PATH to be able to run VEP scripts./n By default MutsigCV is disabled. If you want to enable it you have to first download and install [Matlab Runtime](http://es.mathworks.com/products/compiler/mcr/) and MutsigCV](https://www.broadinstitute.org/cancer/cga/mutsig) and then edit the IntOGen configuration file that by default it's at /.intogen/system.conf (parameters: mutsig_enabled, mutsig_path and matlab_mcr) /nInstallation: To install or update to the last stable version of IntOGen you need to run: /n $ pip install intogen pandas=0.17/nAfter this you will have the `intogen` script available at your path and if this is the first time that you install IntOGen you need to run the setup to download all the data dependencies. This setup will download 3.6Gb of data that after uncompress it will need 9Gb of free space. /n $ intogen --setup/n**TIP**: By default the IntOGen configuration files are in `/.intogen` if you want to change this folder you need to define/nthe system environment variable **INTOGEN_HOME** using the `export` command. Also, all the datasets are downloaded by/ndefault at `/.bgdata` if you want to change this folder you need to define the system environment variable **BGDATA_LOCAL**./nRun an example:/nDownload and extract some samples VCF files:/n $ wget https://bitbucket.org/intogen/intogen-pipeline/downloads/intogen-samples.tar.gz/n $ tar xvzf intogen-samples.tar.gz /nRun IntOGen using the default tasks configuration./n $ intogen -i sample1.vcf -i sample2.vcf -i sample3.vcf -i sample4.vcf /nBrowse the results at the `output` folder./n /nCustom configuration:/nAt `/.intogen/task.conf` you can check the default task configuration values. If you want to run the pipeline /nusing different parameters you can change the default values or create a `.smconfig` file for each project. /nThe `.smconfig` files are a copy of `/.intogen/task.conf` but adding `id` and `files` parameters. The `id` is the name /nof the project and the `files` is a list separated by comma of all the files (MAF, VCF or tab format) that contain /nsamples for that project. /nYou can create a `.smconfig` file like this:/n $ echo -e "id = allsamples/nfiles = sample1.vcf,sample2.vcf,sample3.vcf,sample4.vcf/n" > allsamples.smconfig/n $ cat /.intogen/task.conf >> allsamples.smconfig/nTo run it again, you need to delete or move the previous output and run using the `.smconfig` file as input./n $ rm -rf output/n $ intogen -i allsamples.smconfig /nIf you want to run multiple projects at once you can create multiple `.smconfig` files in one folder and then give that/nfolder as input.
Analyses somatic mutations in thousands of tumor genomes to identify cancer driver genes.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2016-12-21T11:51:09Z/nNo. of bitstreams: 1/nintogen-pipeline.zip: 128015 bytes, checksum: a735d843d32c710fa77764a32037ac87 (MD5)
Made available in DSpace on 2016-12-21T11:51:09Z (GMT). No. of bitstreams: 1/nintogen-pipeline.zip: 128015 bytes, checksum: a735d843d32c710fa77764a32037ac87 (MD5)/n Previous issue date: 2016-07-18
eng
Universitat Pompeu Fabra
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013; 10 (11): 1081-2. DOI: 10.1038/nmeth.2642
Més informació: IntOGen pipeline (Bitbucket)
http://dx.doi.org/10.1038/nmeth.2642
https://bitbucket.org/intogen/intogen-pipeline
IntOGen Mutations Analysis is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto. Copyright® 2012-2014 Universitat Pompeu Fabra./nIntOGen Mutations Analysis is made available to the general public subject to certain conditions described in its license. For the avoidance of doubt, you may use the software and any data accessed through UPF software for academic, non-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter in any way for commercial purposes, or for the purpose of redistribution, without a license from the Universitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or redistribution of IntOGen Mutations Analysis may be sent via e-mail to innovacio@upf.edu./nThird Party Software - Third Party Data/nThe following software may be included in the code and, unless otherwise specified, is licensed under the licenses described below. The disclaimers and copyright notices provided are based on information made available to UPF by the third party licensors listed:/n- VEP/n- Ensembl/n- LiftOver/nRegarding third-party data, you agree to comply with the terms and conditions described in the licenses provided below, based on information made available to UPF by the third party licensors listed:/n- Ensembl genes: www.ensembl.org European Bioinformatic Institute./n- Mutation assessor 2: www.mutationassessor.org Computational Biology Center/n- Memorial Sloan Kettering Cancer Center./n- KEGG: http://www.genome.jp/kegg//n- Gene Ontology: http://www.geneontology.org//n- ICGC: http://icgc.org//n- TCGA: http://cancergenome.nih.gov//nAll rights in any third-party data and/or any third-party software, including all ownership rights, are reserved and remain with the respective third parties. You agree that these third parties may enforce their rights under this agreement against you directly in their own name.
http://bg.upf.edu/licenses/intogen-mutations-analysis-license.txt
info:eu-repo/semantics/openAccess
IntOGen - Pipeline
info:eu-repo/semantics/other
Software
Cancer genes
Cancer
Mutation analysis
Gene drive
ORIGINAL
intogen-pipeline.zip
intogen-pipeline.zip
application/octet-stream
128015
http://repositori.upf.edu/bitstream/10230/27810/1/intogen-pipeline.zip
a735d843d32c710fa77764a32037ac87
MD5
1
10230/27810
oai:repositori.upf.edu:10230/27810
2017-02-03 13:21:32.26
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/278782018-02-19T12:30:04Zcom_10230_5963col_10230_24644
Pérez Llamas, Christian, 1976-
López Bigas, Núria
Schroeder, Michael Philipp, 1986-
Déu Pons, Jordi
2017-01-12T12:31:19Z
2017-01-12T12:31:19Z
2016-07-05
http://hdl.handle.net/10230/27878
Software: Java 7+
Gitools is a framework for analysis and visualization of multidimensional genomic data using interactive heat-maps
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-12T12:31:19Z/nNo. of bitstreams: 1/ngitools.zip: 33563446 bytes, checksum: 292d075e3750bafbad97567e0c386456 (MD5)
Made available in DSpace on 2017-01-12T12:31:19Z (GMT). No. of bitstreams: 1/ngitools.zip: 33563446 bytes, checksum: 292d075e3750bafbad97567e0c386456 (MD5)/n Previous issue date: 2016-07-05
eng
Universitat Pompeu Fabra
Publicació relacionada: Pérez-Llamas C, López-Bigas N. Gitools: analysis and visualisation of genomic data using interactive heat-maps. PLoS ONE. 2011; 6(5): e19541. DOI 10.1371/journal.pone.0019541 http://hdl.handle.net/10230/23502
Més informació: Gitools website
http://hdl.handle.net/10230/23502
http://www.gitools.org/
GNU General Public License v3.0. Consulteu les condicions d'ús específiques dins del document
http://www.gnu.org/licenses/gpl-3.0.txt
info:eu-repo/semantics/openAccess
Gitools
info:eu-repo/semantics/other
Software
Visualization
Heatmap
ORIGINAL
gitools.zip
gitools.zip
application/octet-stream
33563446
http://repositori.upf.edu/bitstream/10230/27878/1/gitools.zip
292d075e3750bafbad97567e0c386456
MD5
1
10230/27878
oai:repositori.upf.edu:10230/27878
2018-02-19 13:30:04.196
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/279282017-01-18T11:54:06Zcom_10230_5963col_10230_24644
Mularoni, Loris
Sabarinathan, Radhakrishnan
González-Pérez, Abel
López Bigas, Núria
Déu Pons, Jordi
2017-01-18T10:13:50Z
2017-01-18T10:13:50Z
2016-06-06
http://hdl.handle.net/10230/27928
Software: Python3+
Method to identify genomic regions, both coding and non-coding, bearing mutations with significant shift towards high functional impact across a cohort of tumos (FMbias), which are candidates to function as cancer drivers, through a local test.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-18T10:13:50Z/nNo. of bitstreams: 1/noncodrivefml.zip: 1601418 bytes, checksum: 75850a7d8983c5cd3c740b3c3af63eb5 (MD5)
Made available in DSpace on 2017-01-18T10:13:50Z (GMT). No. of bitstreams: 1/noncodrivefml.zip: 1601418 bytes, checksum: 75850a7d8983c5cd3c740b3c3af63eb5 (MD5)/n Previous issue date: 2016-06-06
eng
Universitat Pompeu Fabra
Més informació: OncodriveFML (Bitbucket)
Mularoni L, Sabarinathan R, Déu Pons J, González-Pérez A, López Bigas N. OncodriveFML: a general framework to identify coding and non-coding regions with cancer driver mutations. Genome Biology. 2016; 17:128. DOI: 10.1186/s13059-016-0994-0 http://hdl.handle.net/10230/27626
http://hdl.handle.net/10230/27626
http://bitbucket.org/bbglab/oncodrivefml
OncodriveFML is the property of the Universitat Pompeu Fabra (UPF), which hold the copyright thereto./nCopyright® 2012-2014 Universitat Pompeu Fabra./nOncodriveFML is made available to the general public subject to certain conditions described in its license./nFor the avoidance of doubt, you may use the software and any data accessed through UPF software for academic,/nnon-commercial and personal use only, and you may not copy, distribute, transmit, duplicate, reduce or alter/nin any way for commercial purposes, or for the purpose of redistribution, without a license from the/nUniversitat Pompeu Fabra (UPF). Requests for information regarding a license for commercial use or/nredistribution of OncodriveFML may be sent via e-mail to innovacio@upf.edu./nThird Party Software/nThe third-party software listed below is downloaded directly from its homepages and, unless otherwise specified,/nis licensed under the licenses described below. The disclaimers and copyright notices provided are based on/ninformation made available to UPF by the third party licensors listed:/nNumpy: http://www.numpy.org//nScipy: http://www.scipy.org//nPandas: https://github.com/pydata/pandas/nStatmodels: http://statsmodels.sourceforge.net//nAll rights in any third-party data and/or any third-party software, including all ownership rights, are reserved/nand remain with the respective third parties. You agree that these third parties may enforce their rights under/nthis agreement against you directly in their own name./nConsulteu les condicions d'ús específiques dins del document.
info:eu-repo/semantics/openAccess
OncodriveFML
info:eu-repo/semantics/other
Software
Cancer
Genome
Driver
Functional mutations
Non-coding
ORIGINAL
oncodrivefml.zip
oncodrivefml.zip
application/octet-stream
1601418
http://repositori.upf.edu/bitstream/10230/27928/1/oncodrivefml.zip
75850a7d8983c5cd3c740b3c3af63eb5
MD5
1
10230/27928
oai:repositori.upf.edu:10230/27928
2017-01-18 12:54:06.298
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/279372017-01-19T09:56:53Zcom_10230_5963col_10230_24644
Déu Pons, Jordi
2017-01-19T09:53:33Z
2017-01-19T09:53:33Z
2016-04
http://hdl.handle.net/10230/27937
Software: Pyton 3+
Python tab files parsing and validating schema tools.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-19T09:53:33Z/nNo. of bitstreams: 1/nitab.zip: 17569 bytes, checksum: 37f336f9628cd03712f465ca9964959e (MD5)
Made available in DSpace on 2017-01-19T09:53:33Z (GMT). No. of bitstreams: 1/nitab.zip: 17569 bytes, checksum: 37f336f9628cd03712f465ca9964959e (MD5)/n Previous issue date: 2016-04
eng
Universitat Pompeu Fabra
Més informació: itab (GitHub)
https://github.com/bbglab/itab
Copyright 2015 Universitat Pompeu Fabra/nLicensed under the Apache License, Version 2.0 (the "License");/nyou may not use this file except in compliance with the License./nYou may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0/nUnless required by applicable law or agreed to in writing, software/ndistributed under the License is distributed on an "AS IS" BASIS,/nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and/nlimitations under the License.
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
itab
info:eu-repo/semantics/other
Software
Tabbulated file parser
ORIGINAL
itab.zip
itab.zip
application/octet-stream
17569
http://repositori.upf.edu/bitstream/10230/27937/1/itab.zip
37f336f9628cd03712f465ca9964959e
MD5
1
10230/27937
oai:repositori.upf.edu:10230/27937
2017-01-19 10:56:53.689
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/279382017-03-15T09:12:48Zcom_10230_5963col_10230_24644
Schroeder, Michael Philipp, 1986-
2017-01-19T10:42:56Z
2017-01-19T10:42:56Z
2015-11
http://hdl.handle.net/10230/27938
Software: Javascript.
A needle-plot (aka stem-plot or lollipop-plot) plots each data point as a big dot and adds a vertical line that makes it appear like a needle.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-19T10:42:56Z/nNo. of bitstreams: 1/nmuts-needle-plot.zip: 269966 bytes, checksum: d7b92e1821fbe6f272a00b22e45cac24 (MD5)
Made available in DSpace on 2017-01-19T10:42:56Z (GMT). No. of bitstreams: 1/nmuts-needle-plot.zip: 269966 bytes, checksum: d7b92e1821fbe6f272a00b22e45cac24 (MD5)/n Previous issue date: 2015-11
eng
Universitat Pompeu Fabra
Més informació: muts-needle-plot (GitHub)
https://github.com/bbglab/muts-needle-plot
Copyright 2015 Universitat Pompeu Fabra/nLicensed under the Apache License, Version 2.0 (the "License");/nyou may not use this file except in compliance with the License./nYou may obtain a copy of the License at/nhttp://www.apache.org/licenses/LICENSE-2.0/nUnless required by applicable law or agreed to in writing, software/ndistributed under the License is distributed on an "AS IS" BASIS,/nWITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and/nlimitations under the License.
info:eu-repo/semantics/openAccess
Mutations Needle Plot (muts-needle-plot)
info:eu-repo/semantics/other
Software
Genomic plot
ORIGINAL
muts-needle-plot.zip
muts-needle-plot.zip
application/octet-stream
269966
http://repositori.upf.edu/bitstream/10230/27938/1/muts-needle-plot.zip
d7b92e1821fbe6f272a00b22e45cac24
MD5
1
10230/27938
oai:repositori.upf.edu:10230/27938
2017-03-15 10:12:48.586
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/279832017-03-08T10:46:44Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
González-Pérez, Abel
López Bigas, Núria
2017-01-25T11:06:22Z
2017-01-25T11:06:22Z
2015-11
http://hdl.handle.net/10230/27983
OncodriveCLUST depends on Python 3 and some external libraries, numpy, scipy, pandas and statsmodels./nThe easiest way to install all this software stack is using the well known Anaconda Python distribution./nThen to get OncodriveCLUST installed run the following command:/n(env) $ pip install oncodriveclust/nAnd that's all. The following command will allow you to check that is correctly installed by showing the command help:/n(env) $ oncodriveclust --help/nusage: oncodriveclust [-h] [--version] [-o PATH] [--cgc PATH] [-m INT] [-c]/n [-p INT]/n NON-SYN-PATH SYN-PATH GENE-TRANSCRIPTS/nRun OncodriveCLUST analysis/npositional arguments:/n NON-SYN-PATH The path to the NON-Synonymous mutations file to be/n checked/n SYN-PATH The path to the Synonymous mutations file to construct/n the background model/n GENE-TRANSCRIPTS The path of a file containing transcripts length for/n genes/noptional arguments:/n -h, --help show this help message and exit/n --version show program's version number and exit/n -o PATH, --out PATH Define the output file path/n --cgc PATH The path of a file containing CGC data/n -m INT, --muts INT Minimum number of mutations of a gene to be included/n in the analysis ('5' by default)/n -c, --coord Use this argument for printing cluster coordinates in/n the output file/n --pos INT AA position column index ('-1' by default)/n -d INT, --dist INT Intra cluster maximum distance ('5' by default)/n -p FLOAT, --prob FLOAT/n Probability of the binomial model to find cluster/n seeds ('0.01' by default)/n --dom PATH The path of a file containing gene domains/n -L LEVEL, --log-level LEVEL/n Define the loggging level
OncodriveCLUST is a method aimed to identify genes whose mutations are biased towards a large spatial clustering. This method is designed to exploit the feature that mutations in cancer genes, especially oncogenes, often cluster in particular positions of the protein. We consider this as a sign that mutations in these regions change the function of these proteins in a manner that provides an adaptive advantage to cancer cells and consequently are positively selected during clonal evolution of tumours, and this property can thus be used to nominate novel candidate driver genes./nThe method does not assume that the baseline mutation probability is homogeneous across all gene positions but it creates a background model using silent mutations. Coding silent mutations are supposed to be under no positive selection and may reflect the baseline clustering of somatic mutations. Given recent evidences of non-random mutation processes along the genome, the assumption of homogenous mutation probabilities is likely an oversimplication introducing bias in the detection of meaningful events.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-25T11:06:22Z/nNo. of bitstreams: 1/noncodriveclust.zip: 936632 bytes, checksum: d0d142a2a553f7d6792da5acf3b1d6e2 (MD5)
Made available in DSpace on 2017-01-25T11:06:22Z (GMT). No. of bitstreams: 1/noncodriveclust.zip: 936632 bytes, checksum: d0d142a2a553f7d6792da5acf3b1d6e2 (MD5)/n Previous issue date: 2015-11
eng
Universitat Pompeu Fabra
Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveCLUST: exploiting the positional clustering of somatic mutations to identify cancer genes. Bioinformatics. 2013; 19(18): 2238-44. DOI: 10.1093/bioinformatics/btt395
Més informació: OncodriveCLUST (Bitbucket)
http://dx.doi.org/10.1093/bioinformatics/btt395
http://bitbucket.org/bbglab/oncodriveclust
Universitat Pompeu Fabra Free Source Code License Agreement. Consulteu les condicions d'ús específiques dins del document.
info:eu-repo/semantics/openAccess
OncodriveCLUST
info:eu-repo/semantics/other
Software
Cancer
Genes
Mutation
Clustering
ORIGINAL
oncodriveclust.zip
oncodriveclust.zip
application/octet-stream
936632
http://repositori.upf.edu/bitstream/10230/27983/1/oncodriveclust.zip
d0d142a2a553f7d6792da5acf3b1d6e2
MD5
1
10230/27983
oai:repositori.upf.edu:10230/27983
2017-03-08 11:46:44.266
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/279942017-03-08T10:47:20Zcom_10230_5963col_10230_24644
González-Pérez, Abel
López Bigas, Núria
2017-01-26T10:45:34Z
2017-01-26T10:45:34Z
2015-10
http://hdl.handle.net/10230/27994
OncodriveFM depends on Python 3 and some external libraries, numpy, scipy, pandas and statsmodels./nThe easiest way to install all this software stack is using the well known Anaconda Python distribution./nThen to get OncodriveFM installed run the following command:/n(env) $ pip install oncodrivefm/nAnd that's all. The following command will allow you to check that is correctly installed by showing the command help:/n(env) $ oncodrivefm --help/nusage: oncodrivefm [-h] [-o PATH] [-n NAME] [--output-format FORMAT]/n [-N NUMBER] [-e ESTIMATOR] [--gt THRESHOLD]/n [--pt THRESHOLD] [-s SLICES] [-m PATH] [--save-data]/n [--save-analysis] [-j CORES] [-D KEY=VALUE] [-L LEVEL]/n DATA/nCompute the FM bias for genes and pathways/npositional arguments:/n DATA File containing the data matrix in TDM format/noptional arguments:/n -h, --help show this help message and exit/n -o PATH, --output-path PATH/n Directory where output files will be written/n -n NAME Analysis name/n --output-format FORMAT/n The FORMAT for the output file/n -N NUMBER, --samplings NUMBER/n Number of samplings to compute the FM bias pvalue/n -e ESTIMATOR, --estimator ESTIMATOR/n Test estimator for computation./n --gt THRESHOLD, --gene-threshold THRESHOLD/n Minimum number of mutations per gene to compute the FM/n bias/n --pt THRESHOLD, --pathway-threshold THRESHOLD/n Minimum number of mutations per pathway to compute the/n FM bias/n -s SLICES, --slices SLICES/n Slices to process separated by commas/n -m PATH, --mapping PATH/n File with mappings between genes and pathways to be/n analysed/n --save-data The input data matrix will be saved/n --save-analysis The analysis results will be saved/n -j CORES, --cores CORES/n Number of cores to use for calculations. Default is 0/n that means all the available cores/n -D KEY=VALUE Define external parameters to be saved in the results/n -L LEVEL, --log-level LEVEL/n Define log level: debug, info, warn, error, critical,/n notset
OncodriveFM detects candidate cancer driver genes and pathways from catalogs of somatic mutations in a cohort of tumors by computing the bias towards the accumulation of functional mutations (FM bias).This novel approach avoids some known limitations of recurrence-based approaches, such as the difficulty to estimate background mutation rate, and the fact that they usually fail to identify lowly recurrently mutated driver genes.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-26T10:45:34Z/nNo. of bitstreams: 1/noncodriveFM.zip: 111967 bytes, checksum: 5d0e319cc44085bbdd7dae5f5ad1b075 (MD5)
Made available in DSpace on 2017-01-26T10:45:34Z (GMT). No. of bitstreams: 1/noncodriveFM.zip: 111967 bytes, checksum: 5d0e319cc44085bbdd7dae5f5ad1b075 (MD5)/n Previous issue date: 2015-10
eng
Universitat Pompeu Fabra
Gonzalez-Perez A, Lopez-Bigas N. Functional impact bias reveals cancer drivers. Nucleic Acids Research. 2012; 40(21): e169. DOI 10.1093/nar/gks743 http://hdl.handle.net/10230/23344
Més informació: OncodriveFM (Bitbucket)
http://hdl.handle.net/10230/23344
https://bitbucket.org/bbglab/oncodrivefm
Universitat Pompeu Fabra Free Source Code License Agreement. Consulteu les condicions d'ús específiques dins del document.
info:eu-repo/semantics/openAccess
OncodriveFM
info:eu-repo/semantics/other
Software
Cancer
Genes
Driver
Functional mutations
ORIGINAL
oncodriveFM.zip
oncodriveFM.zip
application/octet-stream
111967
http://repositori.upf.edu/bitstream/10230/27994/1/oncodriveFM.zip
5d0e319cc44085bbdd7dae5f5ad1b075
MD5
1
10230/27994
oai:repositori.upf.edu:10230/27994
2017-03-08 11:47:20.911
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280492017-03-10T02:30:28Zcom_10230_5963col_10230_24644
Rubio Pérez, Carlota
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Antolín Hernández, Albert, 1984-
Déu Pons, Jordi
Pérez Llamas, Christian, 1976-
Mestres i López, Jordi
González-Pérez, Abel
López Bigas, Núria
2017-02-03T11:59:10Z
2017-02-03T11:59:10Z
2015-03
http://hdl.handle.net/10230/28049
File contents/n-----------------/nTumor_cohort_details.tsv/nDatasets of somatic mutations employed in the analysis to detect drivers/nCNA_drivers_per_tumor_type.tsv/nList of 29 CNA cancer driver genes in TCGA cohort./nFusion_drivers_per_tumor_type.tsv/nList of 10 fusion driver genes in TCGA cohort./nMutational_drivers_per_tumor_type.tsv/nList of 459 mutation driver genes in full cohort./nMutational_drivers_project_detection.tsv/nList of 459 mutation driver genes detected by project./nMutational_drivers_signals.tsv/nList of genes with at least 1 signal of positive selection across the 6792 samples./nMutational_drivers_count_frequency.tsv/n List of 459 mutational drivers the count of mutated samples across all tumor types./nDrivers_type_role.tsv/nList of 475 drivers, driver type (mutational, CNA and/or fusion driver) and its role in cancer/nDrivers_cloncal_frequency.tsv/nList of 666 genes for which we were able to compute clonal frequency
This database contains information on the genes identified as drivers in Rubio-Perez and Tamborero et al. (2015). It contains information on driver identification at mutational, CNA and gene fusion level. Additional ancillary information about the role and major clonality of drivers is also included. A table is also provided with the list of datasets used for mutational driver identification.
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eng
Universitat Pompeu Fabra
Més informació: IntOGen (web)
Rubio-Perez C, Tamborero D, Schroeder MP, Aantolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015; 27(3): 382-96. DOI: 10.1016/j.ccell.2015.02.007
http://dx.doi.org/10.1016/j.ccell.2015.02.007
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
IntOGen - Cancer Drivers Database (2014)
info:eu-repo/semantics/other
Dataset
Driver
Oncogenic
Cancer genes database
ORIGINAL
CNA_drivers_per_tumor_type.tsv
CNA_drivers_per_tumor_type.tsv
application/octet-stream
1994
http://repositori.upf.edu/bitstream/10230/28049/1/CNA_drivers_per_tumor_type.tsv
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MD5
1
Drivers_clonal_frequency.tsv
Drivers_clonal_frequency.tsv
application/octet-stream
49264
http://repositori.upf.edu/bitstream/10230/28049/2/Drivers_clonal_frequency.tsv
c3126b82ece87bafa85e764d58cfd5c2
MD5
2
Drivers_type_role.tsv
Drivers_type_role.tsv
application/octet-stream
17330
http://repositori.upf.edu/bitstream/10230/28049/3/Drivers_type_role.tsv
08a420fbb0c706418492c44ca7724d6c
MD5
3
Fusion_drivers_per_tumor_type.tsv
Fusion_drivers_per_tumor_type.tsv
application/octet-stream
933
http://repositori.upf.edu/bitstream/10230/28049/4/Fusion_drivers_per_tumor_type.tsv
2d804151bf460ed89f23f223fc3caeca
MD5
4
Mutational_drivers_per_tumor_type.tsv
Mutational_drivers_per_tumor_type.tsv
application/octet-stream
24540
http://repositori.upf.edu/bitstream/10230/28049/5/Mutational_drivers_per_tumor_type.tsv
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MD5
5
Mutational_drivers_project_detection.tsv
Mutational_drivers_project_detection.tsv
application/octet-stream
385478
http://repositori.upf.edu/bitstream/10230/28049/6/Mutational_drivers_project_detection.tsv
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MD5
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Mutational_drivers_signals.tsv
Mutational_drivers_signals.tsv
application/octet-stream
81340
http://repositori.upf.edu/bitstream/10230/28049/7/Mutational_drivers_signals.tsv
fc227a293ba6fb42da9ff5a1923177b3
MD5
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Tumor_cohort_details.tsv
Tumor_cohort_details.tsv
application/octet-stream
4929
http://repositori.upf.edu/bitstream/10230/28049/8/Tumor_cohort_details.tsv
4aeba91d02dc5d97b88785e05827bd36
MD5
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README.txt
README.txt
text/plain
943
http://repositori.upf.edu/bitstream/10230/28049/9/README.txt
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MD5
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LICENSE.txt
LICENSE.txt
text/plain
4109
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MD5
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TEXT
README.txt.txt
README.txt.txt
Extracted text
text/plain
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http://repositori.upf.edu/bitstream/10230/28049/10/README.txt.txt
636d292fc3a5b61700a004d909e03a18
MD5
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LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
4062
http://repositori.upf.edu/bitstream/10230/28049/12/LICENSE.txt.txt
66869d16ea06ce0689b3a2735d1abb65
MD5
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10230/28049
oai:repositori.upf.edu:10230/28049
2017-03-10 03:30:28.501
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280502018-01-24T08:33:12Zcom_10230_5963col_10230_24644
Rubio Pérez, Carlota
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Antolín Hernández, Albert, 1984-
Déu Pons, Jordi
Pérez Llamas, Christian, 1976-
Mestres i López, Jordi
González-Pérez, Abel
López Bigas, Núria
2017-02-03T12:08:31Z
2017-02-03T12:08:31Z
2015-03
http://hdl.handle.net/10230/28050
File contents/n-----------------/nProtein_Drug_Interactions.tsv/nInteractions of 96/475 cancer driver genes in Drivers Database with therapeutic agents/nProtein_druggability.tsv/nExclusvie druggability of 157/475 driver genes according interactions in Protein_Drug_Interactions.tsv/nDrug_details.tsv/nDescription of each drug/nDrug_FDAapproved_rules.tsv/nRules for prescription of FDA approved drugs to genomic alterations/nDrug_ClinicalTrials_rules.tsv/nRules for prescription of drugs in clinical trials to genomic alterations/nDrug_resistances_rules.tsv/nRules for not prescribing drugs to samples bearing genomic alterations of primary resistance/n/nSpecificities/n-----------------/n*In most of the files tumor types are represented through its acronyms (see Drivers Database)/n*Specific genomic dependencies/evidences/resistances are codified in the same unified code in the Columns () in the files (Drug_resistances_rules.tsv, Drug_FDAapproved_rules.tsv, Drug_ClinicalTrials_rules.tsv). /nThe coding rules are:/n- All of them are divided in mutations/CNAs/fusions. /n- For each one, different genes with alterations are semicolon (;) divided./n- Each gene differs from its alterions with colon(:) and its different alterations are comma (,) divided. /ni.e BRAF:V600E,V600K (two diferent alterations)/n- For CNAs A stants for Amplification and D for delention./ni.e. FGFR1:A/n- For mutations all of them are specified at protein level lik referenceAA+proteinposition+alteredAA./ni.e. BRAF:V600E,V600K/n except mutational requirements not based on AA change but specific consequence type, which are specified by ::CT:: after the gene./ni.e. NOTCH1::CT::missense_variant:2380-2445;CT::feature_truncation:2380-2445/n- Fusion partners are divided with dash (-)./ni.e. BCR-ABL1/n- A dot (.) represents any./ni.e. BRAF:V600. (any alteredAA)/ni.e. BRAF:. (any PAM mutation)
This database contains data on the interactions with therapeutic agents an driver genes contained in Cancer Drivers Database (2014.12). It characterizes the interacting therapeutic agents in terms of clinical phase and cancer prescription, among other features. Additionally, it contains ancillary information on specific genomic alterations associated to drug effectiveness which are FDA approved or clinically being tested together with data on other genomic alterations known to be responsible of drug primary resistance.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-03T12:08:31Z/nNo. of bitstreams: 8/ncancer_drivers_actionability-2014.11_scheme.pdf: 601999 bytes, checksum: 34551f510d8bfccba307bdad5c68edcb (MD5)/nREADME.txt: 1857 bytes, checksum: 3bde2d54ede20d6c74b06333ff108186 (MD5)/nDrug_ClinicalTrials_rules.tsv: 1365 bytes, checksum: 498fc218a224decc1da0d8543cf6c20e (MD5)/nDrug_details.tsv: 1331843 bytes, checksum: 3665cbfcf4db5a626c748f34010d1ba8 (MD5)/nDrug_FDAapproved_rules.tsv: 2173 bytes, checksum: fd00581672b4d686eb7ba54f8e19e04d (MD5)/nDrug_resistances_rules.tsv: 2471 bytes, checksum: d31fc20b33263400b9f8a182a00c9ab0 (MD5)/nProtein_Drug_Interactions.tsv: 1645490 bytes, checksum: 44dcc8c59d6609f70f93c811230b63f4 (MD5)/nProtein_druggability.tsv: 5702 bytes, checksum: aea38ebab48d8c2a9fc6aca3c8c12265 (MD5)
Made available in DSpace on 2017-02-03T12:08:31Z (GMT). No. of bitstreams: 8/ncancer_drivers_actionability-2014.11_scheme.pdf: 601999 bytes, checksum: 34551f510d8bfccba307bdad5c68edcb (MD5)/nREADME.txt: 1857 bytes, checksum: 3bde2d54ede20d6c74b06333ff108186 (MD5)/nDrug_ClinicalTrials_rules.tsv: 1365 bytes, checksum: 498fc218a224decc1da0d8543cf6c20e (MD5)/nDrug_details.tsv: 1331843 bytes, checksum: 3665cbfcf4db5a626c748f34010d1ba8 (MD5)/nDrug_FDAapproved_rules.tsv: 2173 bytes, checksum: fd00581672b4d686eb7ba54f8e19e04d (MD5)/nDrug_resistances_rules.tsv: 2471 bytes, checksum: d31fc20b33263400b9f8a182a00c9ab0 (MD5)/nProtein_Drug_Interactions.tsv: 1645490 bytes, checksum: 44dcc8c59d6609f70f93c811230b63f4 (MD5)/nProtein_druggability.tsv: 5702 bytes, checksum: aea38ebab48d8c2a9fc6aca3c8c12265 (MD5)/n Previous issue date: 2015-03
application/pdf
eng
Universitat Pompeu Fabra
Més informació: IntOGen (web)
Rubio-Perez C, Tamborero D, Schroeder MP, Aantolín AA, Deu-Pons J, Perez-Llamas C, Mestres J, Gonzalez-Perez A, Lopez-Bigas N. In silico prescription of anticancer drugs to cohorts of 28 tumor types reveals targeting opportunities. Cancer Cell. 2015; 27(3): 382-96. DOI: 10.1016/j.ccell.2015.02.007
http://dx.doi.org/10.1016/j.ccell.2015.02.007
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
IntOGen - Cancer Drivers Actionability Database
info:eu-repo/semantics/other
Dataset
Cancer driver
Biomarkers
Drugs database
THUMBNAIL
cancer_drivers_actionability-2014.11_scheme.pdf.jpg
cancer_drivers_actionability-2014.11_scheme.pdf.jpg
IM Thumbnail
image/jpeg
9155
http://repositori.upf.edu/bitstream/10230/28050/12/cancer_drivers_actionability-2014.11_scheme.pdf.jpg
1eaf2ff647fb90f3cddab817b789a6ab
MD5
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ORIGINAL
cancer_drivers_actionability-2014.11_scheme.pdf
cancer_drivers_actionability-2014.11_scheme.pdf
application/pdf
601999
http://repositori.upf.edu/bitstream/10230/28050/1/cancer_drivers_actionability-2014.11_scheme.pdf
34551f510d8bfccba307bdad5c68edcb
MD5
1
README.txt
README.txt
text/plain
1857
http://repositori.upf.edu/bitstream/10230/28050/2/README.txt
3bde2d54ede20d6c74b06333ff108186
MD5
2
Drug_ClinicalTrials_rules.tsv
Drug_ClinicalTrials_rules.tsv
application/octet-stream
1365
http://repositori.upf.edu/bitstream/10230/28050/3/Drug_ClinicalTrials_rules.tsv
498fc218a224decc1da0d8543cf6c20e
MD5
3
Drug_details.tsv
Drug_details.tsv
application/octet-stream
1331843
http://repositori.upf.edu/bitstream/10230/28050/4/Drug_details.tsv
3665cbfcf4db5a626c748f34010d1ba8
MD5
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Drug_FDAapproved_rules.tsv
Drug_FDAapproved_rules.tsv
application/octet-stream
2173
http://repositori.upf.edu/bitstream/10230/28050/5/Drug_FDAapproved_rules.tsv
fd00581672b4d686eb7ba54f8e19e04d
MD5
5
Drug_resistances_rules.tsv
Drug_resistances_rules.tsv
application/octet-stream
2471
http://repositori.upf.edu/bitstream/10230/28050/6/Drug_resistances_rules.tsv
d31fc20b33263400b9f8a182a00c9ab0
MD5
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Protein_Drug_Interactions.tsv
Protein_Drug_Interactions.tsv
application/octet-stream
1645490
http://repositori.upf.edu/bitstream/10230/28050/7/Protein_Drug_Interactions.tsv
44dcc8c59d6609f70f93c811230b63f4
MD5
7
Protein_druggability.tsv
Protein_druggability.tsv
application/octet-stream
5702
http://repositori.upf.edu/bitstream/10230/28050/8/Protein_druggability.tsv
aea38ebab48d8c2a9fc6aca3c8c12265
MD5
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LICENSE.txt
LICENSE.txt
text/plain
4109
http://repositori.upf.edu/bitstream/10230/28050/14/LICENSE.txt
f3756c4538671a2402bdd6faa63dd896
MD5
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TEXT
cancer_drivers_actionability-2014.11_scheme.pdf.txt
cancer_drivers_actionability-2014.11_scheme.pdf.txt
Extracted text
text/plain
811
http://repositori.upf.edu/bitstream/10230/28050/11/cancer_drivers_actionability-2014.11_scheme.pdf.txt
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MD5
11
README.txt.txt
README.txt.txt
Extracted text
text/plain
1834
http://repositori.upf.edu/bitstream/10230/28050/13/README.txt.txt
19056b3cad7daed283c4aae0e2c2be67
MD5
13
LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
4062
http://repositori.upf.edu/bitstream/10230/28050/15/LICENSE.txt.txt
66869d16ea06ce0689b3a2735d1abb65
MD5
15
10230/28050
oai:repositori.upf.edu:10230/28050
2018-01-24 09:33:12.282
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280092017-01-27T10:43:02Zcom_10230_5963col_10230_24644
Déu Pons, Jordi
2017-01-27T10:41:25Z
2017-01-27T10:41:25Z
2014-11
http://hdl.handle.net/10230/28009
Software: Java 7+
Onexus is a modular framework to manage the complete life cycle of data analyses. Data analyses follow these steps: analysis definition, analysis execution, results storing, results browsing and finally results publishing.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-01-27T10:41:24Z/nNo. of bitstreams: 1/nonexus.zip: 3425172 bytes, checksum: 27beac87d4308e6fcc24b3cf97e965f1 (MD5)
Made available in DSpace on 2017-01-27T10:41:25Z (GMT). No. of bitstreams: 1/nonexus.zip: 3425172 bytes, checksum: 27beac87d4308e6fcc24b3cf97e965f1 (MD5)/n Previous issue date: 2014-11
eng
Universitat Pompeu Fabra
Més informació: Onexus (GitHub)
https://github.com/onexus/onexus
Copyright 2012 Universitat Pompeu Fabra./n Licensed under the Apache License, Version 2.0 (the "License");/n you may not use this file except in compliance with the License./n You may obtain a copy of the License at/n http://www.apache.org/licenses/LICENSE-2.0/n Unless required by applicable law or agreed to in writing, software/n distributed under the License is distributed on an "AS IS" BASIS,/n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./n See the License for the specific language governing permissions and/n limitations under the License./nConsulteu les condicions d'ús específiques dins del document.
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
Onexus
info:eu-repo/semantics/other
Software
Data analysis framework
ORIGINAL
onexus.zip
onexus.zip
application/octet-stream
3425172
http://repositori.upf.edu/bitstream/10230/28009/1/onexus.zip
27beac87d4308e6fcc24b3cf97e965f1
MD5
1
10230/28009
oai:repositori.upf.edu:10230/28009
2017-01-27 11:43:02.774
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280252017-02-01T10:04:00Zcom_10230_5963col_10230_24644
Pérez Llamas, Christian, 1976-
2017-02-01T10:02:21Z
2017-02-01T10:02:21Z
2014-06
http://hdl.handle.net/10230/28025
Workflows in Wok are defined in an xml file with the .flow extension. This definition includes:/n- the different modules (or pieces of processing)/n- the interconnections between modules (i.e. the input of module B links with the output of module A)/n- explicit dependencies (i.e. module A cannot be executed until module B has finished)/n- descriptions that can be used to generate documentation automatically or to create web forms/nEach module corresponds with a piece of software that has to be run in order to process some input and generate an output. For now, only Python scripts are allowed, but they can be used to execute software written in other languages./nWorkflows in Wok can be treated as any software project and managed with version control system tools and the IDE of your choice./nWok can be used as a terminal script or can be run in server mode./nThe execution of a workflow in the terminal is done using the wok-run script which allows few options:/n- An instance name (-n name), which allows to run the same workflow many times simultaneously independently/n- Configuration files (-c file.conf), the configuration can be splitted in as much files as desired/n- Configuration parameters (-D param=value), which overwrite any previous configuration in configuration files/nThe workflow definition file (i.e. myworkflow.flow) is passed as the first argument./nTo monitor the execution of the workflow there are different resources available:/n- The web server that allows to interact with the engine in a very straightforward way. Recommended!./n- The logs emited by the wok-run through the standard output,/n- The intermediate files generated by Wok (i.e. the tasks output files)/nIt has been designed for workflow developers who feel more confortable programming than doing hundred of clicks and drag & drop's, and also for those who want infraestructure flexibility and full control and monitorization of the execution.
Wok is a workflow management system implemented in Python that makes very easy to structure the workflows, parallelize their execution and monitor its progress among other things. It is designed in a modular way allowing to adapt it to different infraestructures./nFor the time being it is strongly focused on clusters implementing any DRMAA compatible resource manager (i.e. Oracle Grid Engine) which working nodes have a shared folder in common. Other, more flexible infrastructures (such as the Amazon EC2) are considered for future implementations.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-01T10:02:21Z/nNo. of bitstreams: 1/nwok.zip: 550997 bytes, checksum: a6189bb51563691f51a4f3e27cddab73 (MD5)
Made available in DSpace on 2017-02-01T10:02:21Z (GMT). No. of bitstreams: 1/nwok.zip: 550997 bytes, checksum: a6189bb51563691f51a4f3e27cddab73 (MD5)/n Previous issue date: 2014-06
eng
Universitat Pompeu Fabra
Més informació: Wok (GitHut)
http://github.com/bbglab/wok
GNU General Public License v3.0
http://www.gnu.org/licenses/gpl-3.0.en.html
info:eu-repo/semantics/openAccess
Wok
info:eu-repo/semantics/other
Software
Parallell workflow managment system
ORIGINAL
wok.zip
wok.zip
application/octet-stream
550997
http://repositori.upf.edu/bitstream/10230/28025/1/wok.zip
a6189bb51563691f51a4f3e27cddab73
MD5
1
10230/28025
oai:repositori.upf.edu:10230/28025
2017-02-01 11:04:00.723
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280302017-02-01T11:56:15Zcom_10230_5963col_10230_24644
Schroeder, Michael Philipp, 1986-
Rubio Pérez, Carlota
Tamborero Noguera, David
González-Pérez, Abel
López Bigas, Núria
2017-02-01T11:52:55Z
2017-02-01T11:52:55Z
2014-06
http://hdl.handle.net/10230/28030
Software: R
Machine-learning based approach to classify cancer driver genes into to Activating or Loss of Function roles for cancer gene development.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-01T11:52:55Z/nNo. of bitstreams: 1/noncodriverole.zip: 6714157 bytes, checksum: c4f2f940575115d2fbf4560b4b16cd4d (MD5)
Made available in DSpace on 2017-02-01T11:52:55Z (GMT). No. of bitstreams: 1/noncodriverole.zip: 6714157 bytes, checksum: c4f2f940575115d2fbf4560b4b16cd4d (MD5)/n Previous issue date: 2014-06
eng
Universitat Pompeu Fabra
Més informació: OncodriveRole (Bitbucket)
Schroeder MP, Rubio-Perez C, Tamborero D, Gonzalez-Perez A, Lopez-Bigas N. OncodriveROLE classifies cancer driver genes in loss of function and activating mode of action. Bioinformatics. 2014 Sep 1; 30(17): i549-55. DOI: 10.1093/bioinformatics/btu467 http://hdl.handle.net/10230/24768
http://hdl.handle.net/10230/24768
http://bitbucket.org/bbglab/oncodriverole
Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
OncodriveRole
info:eu-repo/semantics/other
Software
Cancer
Genes
Driver
Function classification
ORIGINAL
oncodriverole.zip
oncodriverole.zip
application/octet-stream
6714157
http://repositori.upf.edu/bitstream/10230/28030/1/oncodriverole.zip
c4f2f940575115d2fbf4560b4b16cd4d
MD5
1
10230/28030
oai:repositori.upf.edu:10230/28030
2017-02-01 12:56:15.481
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280332017-02-02T10:37:01Zcom_10230_5963col_10230_24644
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
López Bigas, Núria
2017-02-02T10:28:46Z
2017-02-02T10:28:46Z
2014-03
http://hdl.handle.net/10230/28033
jHeatmap is designed for incorporation into web portals and applications so it has the above listed extension points which may be adapted to the developer's needs: data readers, cell decorators, data aggregation, sorting algorithms and filters./nThree data readers which allow to read tab separated data into the heatmap and annotations respectively are available. A decorator is a function that defines the color scale to use in the heatmap cells. jHeatmap comes with seven implementations fit for different data types. An aggregator is a function that collapses an array of numbers (rows or columns) into a single number. Aggregators are used in combination with the default sorter. Custom complex sorters are also possible, such as the already available MutualExclusiveSorter. Filters can be added to rows and columns as for example the non-significance filter will hide rows or columns that contain no significant p-values.
Javascript library to create interactive heatmaps within webpages.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-02T10:28:46Z/nNo. of bitstreams: 1/njheatmap.zip: 35130167 bytes, checksum: 317df399105bfdb3a9d7a86078611b10 (MD5)
Made available in DSpace on 2017-02-02T10:28:46Z (GMT). No. of bitstreams: 1/njheatmap.zip: 35130167 bytes, checksum: 317df399105bfdb3a9d7a86078611b10 (MD5)/n Previous issue date: 2014-03
eng
Universitat Pompeu Fabra
Més informació: jHeatmap (web)
Deu-Pons J, Schroeder MP, Lopez-Bigas N. jHeatmap: an interactive heatmap viewer for the web. Bioinformatics. 2014; 30(12): 1757-8. DOI: 10.1093/bioinformatics/btu094
http://doi.org/10.1093/bioinformatics/btu094
http://jheatmap.github.io/jheatmap/
Copyright 2011 Universitat Pompeu Fabra (http://www.upf.edu)./n Licensed under the Apache License, Version 2.0 (the "License");/n you may not use this file except in compliance with the License./n You may obtain a copy of the License at/n <http://www.apache.org/licenses/LICENSE-2.0>/n Unless required by applicable law or agreed to in writing, software/n distributed under the License is distributed on an "AS IS" BASIS,/n WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./n See the License for the specific language governing permissions and/n limitations under the License.
http://www.apache.org/licenses/LICENSE-2.0
info:eu-repo/semantics/openAccess
jHeatmap
info:eu-repo/semantics/other
Software
Web heatmaps viewer
ORIGINAL
jheatmap.zip
jheatmap.zip
application/octet-stream
35130167
http://repositori.upf.edu/bitstream/10230/28033/1/jheatmap.zip
317df399105bfdb3a9d7a86078611b10
MD5
1
10230/28033
oai:repositori.upf.edu:10230/28033
2017-02-02 11:37:01.672
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280512017-03-10T02:30:38Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Déu Pons, Jordi
Kandoth, Cyriac
Reimand, Jüri
Lawrence, Michael S.
Getz, Gad
Bader, Gary D.
Ding, Li
López Bigas, Núria
2017-02-03T12:17:03Z
2017-02-03T12:17:03Z
2013-10
http://hdl.handle.net/10230/28051
1 .txt file
This file lists the High Confidence Drivers identified as part of the pan-cancer12 initiative, published in the paper Comprehensive identification of mutational cancer driver genes across 12 tumor types" Scientific Reports 3:2650, 2013, doi:10.1038/srep02650
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-03T12:17:03Z/nNo. of bitstreams: 1/ntcga_pancancer_12_HCD.txt: 16316 bytes, checksum: 3bc10148162adfb9eff5057d62903067 (MD5)
Made available in DSpace on 2017-02-03T12:17:03Z (GMT). No. of bitstreams: 1/ntcga_pancancer_12_HCD.txt: 16316 bytes, checksum: 3bc10148162adfb9eff5057d62903067 (MD5)/n Previous issue date: 2013-10
eng
Universitat Pompeu Fabra
Més informació: IntOGen (web)
Tamborero D, González-Párez A, Pérez-Llamas C, Deu-Pons J, Kandoth C, Reimand J et al. Comprehensive identification of mutational cancer driver genes across 12 tumor types. Scientific Reports. 2013; 3: 2650. DOI 10.1038/srep02650 http://hdl.handle.net/10230/24554
http://hdl.handle.net/10230/24554
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
IntOGen - TCGA pan-cancer12 high confidence drivers
info:eu-repo/semantics/other
Dataset
High confidence drivers
Genes cancer dataset
ORIGINAL
tcga_pancancer_12_HCD.txt
tcga_pancancer_12_HCD.txt
text/plain
16316
http://repositori.upf.edu/bitstream/10230/28051/1/tcga_pancancer_12_HCD.txt
3bc10148162adfb9eff5057d62903067
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LICENSE.txt
LICENSE.txt
text/plain
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http://repositori.upf.edu/bitstream/10230/28051/3/LICENSE.txt
f3756c4538671a2402bdd6faa63dd896
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TEXT
tcga_pancancer_12_HCD.txt.txt
tcga_pancancer_12_HCD.txt.txt
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text/plain
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http://repositori.upf.edu/bitstream/10230/28051/2/tcga_pancancer_12_HCD.txt.txt
c19a142796740609a9ba543314b73fc1
MD5
2
LICENSE.txt.txt
LICENSE.txt.txt
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text/plain
4062
http://repositori.upf.edu/bitstream/10230/28051/4/LICENSE.txt.txt
66869d16ea06ce0689b3a2735d1abb65
MD5
4
10230/28051
oai:repositori.upf.edu:10230/28051
2017-03-10 03:30:38.85
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280482017-02-03T10:15:55Zcom_10230_5963col_10230_24644
Barneda Zahonero, Bruna
Román González, Lidia
Collazo, Olga
Rafati, Haleh
Islam, Abul, 1978-
Bussmann, Lars
Di Tullio, Alessandro, 1982-
Andrés, Luisa De
Graf, T. (Thomas)
López Bigas, Núria
Mahmoudi, Tokameh
Parra, Maribel
2017-02-03T10:11:06Z
2017-02-03T10:11:06Z
2013-05
http://hdl.handle.net/10230/28048
Software: Docker 1.12+
HDAC7 is a repressor of myeloid genes whose downregulation in pre-B cells is required for transdifferentiation into macrophages.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-03T10:11:06Z/nNo. of bitstreams: 1/nc10hdac7.zip: 19356852 bytes, checksum: 2064999e8f159f09e022b34c4dcbaa8f (MD5)
Made available in DSpace on 2017-02-03T10:11:06Z (GMT). No. of bitstreams: 1/nc10hdac7.zip: 19356852 bytes, checksum: 2064999e8f159f09e022b34c4dcbaa8f (MD5)/n Previous issue date: 2013-05
eng
Universitat Pompeu Fabra
Més informació: C10-HDAC7 (web)
Barneda-Zahonero B, Roman-Gonzalez L, Collazo O, Rafati H, Islam ABMMK, Bussmann LH et al. HDAC7 is a repressor of myeloid genes whose downregulation is required for transdifferentiation of pre-B cells into macrophages. PLoS Genetics. 2013; 9(5): e1003503. DOI: 10.1371/journal.pgen.1003503 http://hdl.handle.net/10230/23441
http://hdl.handle.net/10230/23441
http://bg.upf.edu/projects/C10-HDAC7/
Aquest document es troba sota llicència Creative Commons Reconeixement 3.0 Espanya (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
C10-HDAC7
info:eu-repo/semantics/other
Software
hdac7 gene
Mueloid genes
ORIGINAL
c10hdac7.zip
c10hdac7.zip
application/octet-stream
19356852
http://repositori.upf.edu/bitstream/10230/28048/1/c10hdac7.zip
2064999e8f159f09e022b34c4dcbaa8f
MD5
1
10230/28048
oai:repositori.upf.edu:10230/28048
2017-02-03 11:15:55.048
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280812017-03-18T02:30:44Zcom_10230_5963col_10230_24644
González-Pérez, Abel
Pérez Llamas, Christian, 1976-
Déu Pons, Jordi
Tamborero Noguera, David
Schroeder, Michael Philipp, 1986-
Jené i Sanz, Alba, 1984-
Santos, Alberto
López Bigas, Núria
2017-02-08T09:45:50Z
2017-02-08T09:45:50Z
2013-05
http://hdl.handle.net/10230/28081
1 .ZIP file
Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-08T09:45:50Z/nNo. of bitstreams: 1/nintogen_cancer_drivers-2013.zip: 122532213 bytes, checksum: cb430846306df545a1f7b7b30c3f236f (MD5)
Made available in DSpace on 2017-02-08T09:45:50Z (GMT). No. of bitstreams: 1/nintogen_cancer_drivers-2013.zip: 122532213 bytes, checksum: cb430846306df545a1f7b7b30c3f236f (MD5)/n Previous issue date: 2013-05
eng
Universitat Pompeu Fabra
Més informació: IntOGen (web)
Gonzalez-Perez A, Perez-Llamas C, Deu-Pons J, Tamborero D, Schroeder MP, Jene-Sanz A, Santos A, Lopez-Bigas N. IntOGen-mutations identifies cancer drivers across tumor types. Nat Methods. 2013;10(11):1081-2. DOI: 10.1038/nmeth.2642
http://dx.doi.org/10.1038/nmeth.2642
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
IntOGen - Cancer driver database (2013)
info:eu-repo/semantics/other
Dataset
Cancer
Genes
Driver
Database
TEXT
LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
4062
http://repositori.upf.edu/bitstream/10230/28081/3/LICENSE.txt.txt
66869d16ea06ce0689b3a2735d1abb65
MD5
3
ORIGINAL
intogen_cancer_drivers-2013.zip
intogen_cancer_drivers-2013.zip
application/octet-stream
122532213
http://repositori.upf.edu/bitstream/10230/28081/1/intogen_cancer_drivers-2013.zip
cb430846306df545a1f7b7b30c3f236f
MD5
1
LICENSE.txt
LICENSE.txt
text/plain
4109
http://repositori.upf.edu/bitstream/10230/28081/2/LICENSE.txt
f3756c4538671a2402bdd6faa63dd896
MD5
2
10230/28081
oai:repositori.upf.edu:10230/28081
2017-03-18 03:30:44.772
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280822017-02-08T10:12:42Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
López Bigas, Núria
González-Pérez, Abel
2017-02-08T10:09:26Z
2017-02-08T10:09:26Z
2013-02
http://hdl.handle.net/10230/28082
How to install and run/nWe distribute a Python implementation of Oncodrive-CIS in a compressed file below. Oncodrive-CIS requires three input files containing:/nexpression values per sample and per gene/ncopy number status per sample and per gene/na sample file stating whether each sample identifier corresponds to either a normal or a tumor/nOncodrive-CIS is executed by the oncodrivecis.py script. It requires several arguments (some of them optional), which are displayed by typing -h (or --help):/n$ python src/oncodrivecis.py -h /nUsage: oncodrivecis.py [options] /nOptions: /n -h, --help show this help message and exit /n -e PATH, --expression=PATH /n Specifies the path to the exp file /n -c PATH, --cnv=PATH Specifies the path to the CNA file /n -s PATH, --samples=PATH /n Specifies the path to the samples file /n -o PATH, --output=PATH /n Specifies the output folder (by default the same than /n the samples file one) /n -i PATH, --identifier=PATH /n Specifies the gene id conversion file /n (optional) /n -n INT, --nsampling=INT /n Sampling number per gene (optional, 10000 by default) /n -a INT, --alterations=INT /n Minimum number of alterations per gene (2 by default) /nAmong the downloadable files we have included the gliobastoma multiforme data set (see the main manuscript for further details about these data) already formatted to be processed by Oncodrive-CIS. For using it, type the following:/n$ python src/oncodrivecis.py //n -e gbm_data/expression.per.gene.ens.gbm.tsv //n -c gbm_data/cnv.rae.ens.gbm.tsv //n -s gbm_data/samples_to_process.tsv //n -o output -i gbm_data/ensembl63_ensembl2hugo.tsv/nThe execution time for this example can be decreased by lowering the number of permutations performed to retrieve the Z score values by using the –n (--nsampling) argument or reduce the number of processed samples by modifying the 'samples_to_process.tsv' file./nNote that further details about Oncodrive-CIS execution, input files and produced output are contained in a User Manual which is available among the downloadable files.
Oncodrive-CIS is a method aimed to identify those copy number alterations (CNAs) leading to larger in cis expression changes that may be useful in elucidating the role of these aberrations in cancer. This is based on the hypothesis that a gene driving oncogenesis through copy number changes is more prone to bias towards overexpression (or underexpression) as compared to bystanders. The effect of the gene dosage is assessed by observing expression changes not only among tumors but also taking into account normal samples data, when available./nOncodrive-CIS has several potential benefits: first, it did not examine the frequency of the CNAs across samples and therefore the detection of low-recurrent driver alterations was not impaired. Second, amplifications and deletions were evaluated separately to obtain a fair ranking of genes, because the expression change measured in deletions was lower than the one obtained from multi-copy amplifications. Third, the expression of genes in tumor samples was analyzed according to the copy number status but was also compared to normal samples, thus better revealing the gene misregulation role of CNAs in cancer cells. And finally, it should be emphasized that the relationship between expression changes and their functional impact is complex, thus Oncodrive-CIS is proposed as a method to elucidate the role of CNAs in cancer which may be complementary to analyses based on other criteria.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-08T10:09:26Z/nNo. of bitstreams: 1/noncodrivecis.zip: 21183647 bytes, checksum: 966540eff2774434d7434ab24f9209cc (MD5)
Made available in DSpace on 2017-02-08T10:09:26Z (GMT). No. of bitstreams: 1/noncodrivecis.zip: 21183647 bytes, checksum: 966540eff2774434d7434ab24f9209cc (MD5)/n Previous issue date: 2013-02
eng
Universitat Pompeu Fabra
Més informació: Oncodrive-CIS (Biomedical Genomics)
Tamborero D, López-Bigas N, González-Pérez A. Oncodrive-CIS: a method to reveal likely driver genes based on the impact of their copy number changes on expression. PLoS ONE. 2013; 8(2): e55489. DOI 10.1371/journal.pone.0055489 http://hdl.handle.net/10230/23565
http://hdl.handle.net/10230/23565
http://bg.upf.edu/group/projects/oncodrive-cis.php
Dades sita llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Oncodrive-CIS
info:eu-repo/semantics/other
Software
Copy number gene
Significant expression
ORIGINAL
oncodrivecis.zip
oncodrivecis.zip
application/octet-stream
21183647
http://repositori.upf.edu/bitstream/10230/28082/1/oncodrivecis.zip
966540eff2774434d7434ab24f9209cc
MD5
1
10230/28082
oai:repositori.upf.edu:10230/28082
2017-02-08 11:12:42.125
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280952017-02-09T09:10:26Zcom_10230_5963col_10230_24644
Rafael Palou, Xavier
Schroeder, Michael Philipp, 1986-
López Bigas, Núria
2017-02-09T09:05:23Z
2017-02-09T09:05:23Z
2012-01
http://hdl.handle.net/10230/28095
Execution of SVGMap/nThis project provides a Jetty Server to run SVGMap web, which needs Sun Java 1.6 or higher installed on your machine./nIf your Operating System is a Linux or Mac OS X, then execute run.sh, in Windows use run.bat. We strongly recommend to run SVGMap from a terminal by the commands listed below!/nWhen you run SVGMap a Webserver is created at the port 8095. Access to it by opening your favourite browser and direct yourself to the address: http://localhost:8095/nKeep in mind that you may execute SVGMap only once per machine with the same port, otherwise it may create conflicts. The same applies if you already have another service running on that port. You can change the default port in the run.sh/run.bat on the following lines./nLinux/OS X: run.sh/njava -server -Djetty.port=8095 -Dsvgmap.home=data -jar lib/start-6.1.22.jar/nWindows: run.bat/njava -server -Djetty.port=8095 -jar lib/start-6.1.22.jar/nMore information at https://bg.upf.edu/forge/projects/svgmap/wiki/User_documentation
The aim of SVGMap is helping in the visualisation of experimental data which are associated with some graphical representation. Thus SVGMap browser allows to generate images with colored areas corresponding to the chosen data and color scale./nThe data is represented as a table and is searchable. All data as well as the generated images/figures can be exported easily through the interface./nAdditionally the tool allows to manage (add, edit or delete) experiments and configure the front-end user search appearance such as the number of images to be displayed, the scale types to use and more.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-09T09:05:22Z/nNo. of bitstreams: 1/nsvgmap.zip: 3864108 bytes, checksum: e94caad5539545710639e66df40c4f6d (MD5)
Made available in DSpace on 2017-02-09T09:05:23Z (GMT). No. of bitstreams: 1/nsvgmap.zip: 3864108 bytes, checksum: e94caad5539545710639e66df40c4f6d (MD5)/n Previous issue date: 2012-01
eng
Universitat Pompeu Fabra
Més informació: SVGMap (Bitbucket)
Rafael-Palou X, Schroeder MP, Lopez-Bigas N. SVGMap: configurable image browser for experimental data. Bioinformatics. 2011;28(1):119-20. DOI: 10.1093/bioinformatics/btr581
http://dx.doi.org/10.1093/bioinformatics/btr581
http://bitbucket.org/bbglab/svgmap/wiki/Home
Copyright 2011 Universitat Pompeu Fabra./nThis software is open source and is licensed under the Open Software License version 3.0./nYou may obtain a copy of the License at/nhttp://www.opensource.org/licenses/osl-3.0/nThis software also includes image examples licensed under Creative Commons license./nUnless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied./nSee the License for the specific language governing permissions and limitations under the License.
http://www.opensource.org/licenses/osl-3.0
info:eu-repo/semantics/openAccess
SVGMap
info:eu-repo/semantics/other
Software
SVG interactive viewer
ORIGINAL
svgmap.zip
svgmap.zip
application/octet-stream
3864108
http://repositori.upf.edu/bitstream/10230/28095/1/svgmap.zip
e94caad5539545710639e66df40c4f6d
MD5
1
10230/28095
oai:repositori.upf.edu:10230/28095
2017-02-09 10:10:26.397
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/280972017-02-09T11:52:49Zcom_10230_5963col_10230_24644
Pippa, Raffaella
Espinosa Blay, Lluís
Gundem, Gunes
Garcia Escudero, Ramon
Dominguez, Ana
Orlando, S.
Gallastegui, E.
Saiz, Cristina
Besson, Arnaud
Pujol, Maria Jesus
López Bigas, Núria
Paramio, Jesus M.
Bigas Salvans, Anna
Bachs Valldeneu, Oriol
2017-02-09T11:44:37Z
2017-02-09T11:44:37Z
2011-12
http://hdl.handle.net/10230/28097
Software: Docker 1.12+
The cyclin-cdk (cyclin-dependent kinase) inhibitor p27(Kip1) (p27) has a crucial negative role on cell cycle progression. In addition to its classical role as a cyclin-cdk inhibitor, it also performs cyclin-cdk-independent functions as the regulation of cytoskeleton rearrangements and cell motility. p27 deficiency has been associated with tumor aggressiveness and poor clinical outcome, although the mechanisms underlying this participation still remain elusive. We report here a new cellular function of p27 as a transcriptional regulator in association with p130/E2F4 complexes that could be relevant for tumorigenesis. We observed that p27 associates with specific promoters of genes involved in important cellular functions as processing and splicing of RNA, mitochondrial organization and respiration, translation and cell cycle. On these promoters p27 co-localizes with p130, E2F4 and co-repressors as histone deacetylases (HDACs) and mSIN3A. p27 co-immunoprecipitates with these proteins and by affinity chromatography, we demonstrated a direct interaction of p27 with p130 and E2F4 through its carboxyl-half. We have also shown that p130 recruits p27 on the promoters, and there p27 is needed for the subsequent recruitment of HDACs and mSIN3A. Expression microarrays and luciferase assays revealed that p27 behaves as transcriptional repressor of these p27-target genes (p27-TGs). Finally, in human tumors, we established a correlation with overexpression of p27-TGs and poor survival. Thus, this new function of p27 as a transcriptional repressor could have a role in the major aggressiveness of tumors with low levels of p27.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-09T11:44:37Z/nNo. of bitstreams: 1/np27.zip: 627239172 bytes, checksum: ac9f0eff879e13bef0c55ad35f7cd945 (MD5)
Made available in DSpace on 2017-02-09T11:44:37Z (GMT). No. of bitstreams: 1/np27.zip: 627239172 bytes, checksum: ac9f0eff879e13bef0c55ad35f7cd945 (MD5)/n Previous issue date: 2011-12
eng
Universitat Pompeu Fabra
Més informació: Transcriptional regulatory role of p27Kip1 (web)
Pippa R, Espinosa L, Gundem G, García-Escudero R, Dominguez A, Orlando S, Gallastegui E, Saiz C, Besson A, Pujol MJ, López-Bigas N, Paramio JM, Bigas A, Bachs O. p27Kip1 represses transcription by direct interaction with p130/E2F4 at the promoters of target genes. Oncogene. 2012;31(38):4207-20. DOI: 10.1038/onc.2011.582
http://dx.doi.org/10.1038/onc.2011.582
http://bg.upf.edu/p27/home/
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
p27
info:eu-repo/semantics/other
Software
p27Kip1 interaction promoters
ORIGINAL
p27.zip
p27.zip
application/octet-stream
627239172
http://repositori.upf.edu/bitstream/10230/28097/1/p27.zip
ac9f0eff879e13bef0c55ad35f7cd945
MD5
1
10230/28097
oai:repositori.upf.edu:10230/28097
2017-02-09 12:52:49.685
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281072017-03-18T02:30:45Zcom_10230_5963col_10230_24644
Gundem, Gunes
Pérez Llamas, Christian, 1976-
Jené i Sanz, Alba, 1984-
Kedzierska, Anna
Islam, Abul, 1978-
Déu Pons, Jordi
Furney, Simon J.
López Bigas, Núria
2017-02-10T11:45:15Z
2017-02-10T11:45:15Z
2010-02
http://hdl.handle.net/10230/28107
1 zip file
Genes and pathways affected by expression and copy number changes in tumors across projects and cancer types.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-10T11:45:14Z/nNo. of bitstreams: 1/nintogen_arrays-2010.zip: 69065171 bytes, checksum: 9574d06e7dc70010a73bdc0581103134 (MD5)
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eng
Universitat Pompeu Fabra
Més informació: IntOGen (web)
Gundem G, Perez-Llamas C, Jene-Sanz A, Kedzierska A, Islam A, Deu-Pons J, Furney SJ, Lopez-Bigas N. IntOGen: integration and data mining of multidimensional oncogenomic data. Nat Methods. 2010;7(2):92-3. DOI: 10.1038/nmeth0210-92
http://dx.doi.org/10.1038/nmeth0210-92
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
IntOGen - Arrays
info:eu-repo/semantics/other
Dataset
Expression CNA cancer
Genes pathways
Database
TEXT
LICENSE.txt.txt
LICENSE.txt.txt
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4062
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66869d16ea06ce0689b3a2735d1abb65
MD5
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ORIGINAL
intogen_arrays-2010.zip
intogen_arrays-2010.zip
application/octet-stream
69065171
http://repositori.upf.edu/bitstream/10230/28107/1/intogen_arrays-2010.zip
9574d06e7dc70010a73bdc0581103134
MD5
1
LICENSE.txt
LICENSE.txt
text/plain
4109
http://repositori.upf.edu/bitstream/10230/28107/2/LICENSE.txt
f3756c4538671a2402bdd6faa63dd896
MD5
2
10230/28107
oai:repositori.upf.edu:10230/28107
2017-03-18 03:30:45.018
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281252017-02-20T09:55:00Zcom_10230_5963col_10230_24644
López Bigas, Núria
Kisiel, Tomasz A.
DeWaal, Dannielle C.
Holmes, Katherine B.
Volkert, Tom L.
Gupta, Sumeet
Love, Jennifer
Murray, Heather L.
Young, Richard A.
Benevolenskaya, Elizaveta V.
2017-02-20T09:47:13Z
2017-02-20T09:47:13Z
2008-09
http://hdl.handle.net/10230/28125
1 WAR (Web application ARchive) file and 1 SQL (Structured Query Language) file.
Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-20T09:47:13Z
No. of bitstreams: 2
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rbp2.war: 7320645 bytes, checksum: e74639a8c2af75b3274c01bf8fb255cb (MD5)
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rbp2.war: 7320645 bytes, checksum: e74639a8c2af75b3274c01bf8fb255cb (MD5)
Previous issue date: 2008-09
eng
Universitat Pompeu Fabra
Lopez-Bigas N, Kisiel TA, DeWaal DC, Holmes KB, Volkert TL, Gupta S, Love J, Murray HL, Young RA, Benevolenskaya EV. Genome-wide analysis of the H3K4 histone demethylase RBP2 reveals a transcriptional program controlling differentiation. Mol Cell. 2008; 31(4):520–30. DOI: 10.1016/j.molcel.2008.08.004
http://dx.doi.org/10.1016/j.molcel.2008.08.004
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
RBP2
info:eu-repo/semantics/other
Software
H3K4 histone
RBP2
Transcriptional control
ORIGINAL
Analysis.sql
Analysis.sql
SQL file
application/octet-stream
178555218
http://repositori.upf.edu/bitstream/10230/28125/1/Analysis.sql
feedf10eeb59244c91ea56f8eb4395c7
MD5
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rbp2.war
rbp2.war
WAR file
application/octet-stream
7320645
http://repositori.upf.edu/bitstream/10230/28125/2/rbp2.war
e74639a8c2af75b3274c01bf8fb255cb
MD5
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10230/28125
oai:repositori.upf.edu:10230/28125
2017-02-20 10:55:00.663
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281262017-02-21T08:59:36Zcom_10230_5963col_10230_24644
Furney, Simon J.
Madden, Stephen F.
Kisiel, Tomasz A.
Higgins, Desmond G.
López Bigas, Núria
2017-02-20T12:01:15Z
2017-02-20T12:01:15Z
2007-12
http://hdl.handle.net/10230/28126
# Content
cgprop.war -> Java Website application (deploy in tomcat)
cgprop.sql -> MySQL database
# Example Apache Proxy Pass configuration
ProxyPass /cgprop http://bg.upf.edu:8080/cgprop
ProxyPassReverse /cgprop http://bg.upf.edu:8080/cgprop
Cancer gene properties.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-20T12:01:15Z
No. of bitstreams: 3
cgprop.sql: 26213857 bytes, checksum: 796f26367c3ec59467c4101e43c73515 (MD5)
cgprop.war: 3790076 bytes, checksum: c1a915c9f13ed0c63a192b73267f1c15 (MD5)
README.md: 257 bytes, checksum: 4d5e9d048b625df09af74b0190d4688d (MD5)
Made available in DSpace on 2017-02-20T12:01:15Z (GMT). No. of bitstreams: 3
cgprop.sql: 26213857 bytes, checksum: 796f26367c3ec59467c4101e43c73515 (MD5)
cgprop.war: 3790076 bytes, checksum: c1a915c9f13ed0c63a192b73267f1c15 (MD5)
README.md: 257 bytes, checksum: 4d5e9d048b625df09af74b0190d4688d (MD5)
Previous issue date: 2007-12
eng
Universitat Pompeu Fabra
Furney SJ, Higgins DG, Ouzounis CA, López-Bigas N. Structural and functional properties of genes involved in human cancer. BMC Genomics. 2006; 7: 3. DOI: 10.1186/1471-2164-7-3 http://hdl.handle.net/10230/16420
http://hdl.handle.net/10230/16420
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
CGProp
info:eu-repo/semantics/other
Software
Cancer genes regulation evolution
ORIGINAL
cgprop.sql
cgprop.sql
application/octet-stream
26213857
http://repositori.upf.edu/bitstream/10230/28126/1/cgprop.sql
796f26367c3ec59467c4101e43c73515
MD5
1
cgprop.war
cgprop.war
application/octet-stream
3790076
http://repositori.upf.edu/bitstream/10230/28126/2/cgprop.war
c1a915c9f13ed0c63a192b73267f1c15
MD5
2
README.md
README.md
application/octet-stream
257
http://repositori.upf.edu/bitstream/10230/28126/3/README.md
4d5e9d048b625df09af74b0190d4688d
MD5
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10230/28126
oai:repositori.upf.edu:10230/28126
2017-02-21 09:59:36.206
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281272017-02-21T10:23:29Zcom_10230_5963col_10230_24644
Shikhagaie, Medya
López Bigas, Núria
2017-02-21T10:01:04Z
2017-02-21T10:01:04Z
2007-10
http://hdl.handle.net/10230/28127
Software: Docker 1.12+
Web tool for the selection of SNPs from the STAR project with potential functional effect.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-21T10:01:04Z
No. of bitstreams: 1
funcstar.zip: 198769393 bytes, checksum: eddccfc6da0e95cb28e7488e994b716b (MD5)
Made available in DSpace on 2017-02-21T10:01:04Z (GMT). No. of bitstreams: 1
funcstar.zip: 198769393 bytes, checksum: eddccfc6da0e95cb28e7488e994b716b (MD5)
Previous issue date: 2007-10
eng
Universitat Pompeu Fabra
Més informació: funcSTAR (web)
STAR Consortium. SNP and haplotype mapping for genetic analysis in the rat. Nat Genet. 2008;40(5):560-6. DOI: 10.1038/ng.124
http://dx.doi.org/10.1038/ng.124
http://bg.upf.edu/funcSTAR/
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
funcSTAR
info:eu-repo/semantics/other
Software
SNP functional effect
ORIGINAL
funcstar.zip
funcstar.zip
application/octet-stream
198769393
http://repositori.upf.edu/bitstream/10230/28127/1/funcstar.zip
eddccfc6da0e95cb28e7488e994b716b
MD5
1
10230/28127
oai:repositori.upf.edu:10230/28127
2017-02-21 11:23:29.349
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281282017-02-21T11:17:48Zcom_10230_5963col_10230_24644
López Bigas, Núria
De, Subhajyoti
Teichmann, Sarah A.
2017-02-21T11:11:45Z
2017-02-21T11:11:45Z
2007-10
http://hdl.handle.net/10230/28128
1 SQL (Structured Query Language) file and 1 WAR (Web application ARchive) file.
Mutations, genes and pathways involved in tumorigenesis across 4,623 cancer genomes/exomes from 13 cancer sites. IntOGen-mutations identifies cancer drivers across tumor types. Nature Methods 10, 2013, doi:10.1038/nmeth.2642
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-21T11:11:44Z
No. of bitstreams: 2
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evolvability.war: 7815064 bytes, checksum: 3cb247e834f18cea63f973beb9217b26 (MD5)
Made available in DSpace on 2017-02-21T11:11:45Z (GMT). No. of bitstreams: 2
Analysis.sql: 178555218 bytes, checksum: feedf10eeb59244c91ea56f8eb4395c7 (MD5)
evolvability.war: 7815064 bytes, checksum: 3cb247e834f18cea63f973beb9217b26 (MD5)
Previous issue date: 2007-10
eng
Universitat Pompeu Fabra
Lopez-Bigas N, De S, Teichmann SA. Functional protein divergence in the evolution of Homo sapiens. Genome Biol. 2008; 9:R33. DOI: 10.1186/gb-2008-9-2-r33
http://dx.doi.org/10.1186/gb-2008-9-2-r33
Dades en llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Evolvavility
info:eu-repo/semantics/other
Software
Evolution divergence rates
Homo Sapiens
ORIGINAL
Analysis.sql
Analysis.sql
application/octet-stream
178555218
http://repositori.upf.edu/bitstream/10230/28128/1/Analysis.sql
feedf10eeb59244c91ea56f8eb4395c7
MD5
1
evolvability.war
evolvability.war
application/octet-stream
7815064
http://repositori.upf.edu/bitstream/10230/28128/2/evolvability.war
3cb247e834f18cea63f973beb9217b26
MD5
2
10230/28128
oai:repositori.upf.edu:10230/28128
2017-02-21 12:17:48.016
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281292017-02-21T11:56:13Zcom_10230_5963col_10230_24644
Furney, Simon J.
Albà Soler, Mar
López Bigas, Núria
2017-02-21T11:47:00Z
2017-02-21T11:47:00Z
2006-07
http://hdl.handle.net/10230/28129
# Content
dom_rec_prediction.sql -> MySQL database
web/* -> PHP website
Database of human genes prioritized for their probability of involvement in dominant or recessive hereditary diseases.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-21T11:47:00Z
No. of bitstreams: 1
idgp.zip: 2179853 bytes, checksum: e70e360f6beb877127e5d752a6739331 (MD5)
Made available in DSpace on 2017-02-21T11:47:00Z (GMT). No. of bitstreams: 1
idgp.zip: 2179853 bytes, checksum: e70e360f6beb877127e5d752a6739331 (MD5)
Previous issue date: 2006-07
eng
Universitat Pompeu Fabra
Furney SJ, Albà MM, López-Bigas N. Differences in the evolutionary history of disease genes affected by dominant or recessive mutations. BMC Genomics. 2006; 7: 165. DOI: 10.1186/1471-2164-7-165 http://hdl.handle.net/10230/16419
http://hdl.handle.net/10230/16419
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
iDGP
info:eu-repo/semantics/other
Software
Human gene
Hereditary diseases
ORIGINAL
idgp.zip
idgp.zip
application/octet-stream
2179853
http://repositori.upf.edu/bitstream/10230/28129/1/idgp.zip
e70e360f6beb877127e5d752a6739331
MD5
1
10230/28129
oai:repositori.upf.edu:10230/28129
2017-02-21 12:56:13.701
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281312017-03-18T02:33:04Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
2017-02-22T12:41:22Z
2017-02-22T12:41:22Z
2016-01
http://hdl.handle.net/10230/28131
INSTALL
# Create a new Anaconda python environment with all the required dependencies
$ conda create -c bioconda -c bbglab -n oncodrivemut python=3.5 numpy=1.11 pandas=0.17 colorama=0.3 ago requests=2.11 pytabix=0.1 itab=0.9 bgconfig=0.3
$ source activate oncodrivemut
$ pip install oncodrivemut-1.0.0.tar.gz --no-deps
# The first time that you run OncodriveMUT it will download all the required datasets using bgdata (https://bitbucket.org/bgframework/bgdata)
# by default bgdata downloads all the files at ~/.bgdata check the documentation if you can to change this behaviour
$ oncodrivemut -h
usage: oncodrivemut [-h] -i INPUT_FILE [-o OUTPUT_FOLDER] [-t TUMOR_TYPE]
[-c CONFIG_FILE] [-s SAMPLE] [--force] [--debug]
[--extended]
optional arguments:
-h, --help show this help message and exit
-i INPUT_FILE, --input INPUT_FILE
Variants file
-o OUTPUT_FOLDER, --output OUTPUT_FOLDER
Output folder. Default to regions file name without
extensions.
-t TUMOR_TYPE, --tumor TUMOR_TYPE
Specify the tumor type of the sample(s) under analysis
-c CONFIG_FILE, --config CONFIG_FILE
Configuration file. Default to 'oncodrivemut.conf' in
the current folder if exists or to
~/.bbglab/oncodrivemut.conf if not.
-s SAMPLE, --sample SAMPLE
Default identifier of the sample
--force Run the commands and overwrite results although output
files already exist
--debug Show more progress details
--extended Computational expensive metrics are also calculated
for non coding mutations
Bioinformatics method to identify individual driver mutations.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-22T12:41:22Z
No. of bitstreams: 1
oncodrivemut.zip: 43022 bytes, checksum: 3e299fc12b2cb0eb858fe632ec442171 (MD5)
Made available in DSpace on 2017-02-22T12:41:22Z (GMT). No. of bitstreams: 1
oncodrivemut.zip: 43022 bytes, checksum: 3e299fc12b2cb0eb858fe632ec442171 (MD5)
Previous issue date: 2016-01
eng
Universitat Pompeu Fabra
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://bitbucket.org/intogen/intogen-pipeline/raw/a2569e57124108eabd6695009e8a6a682154e49e/LICENSE
info:eu-repo/semantics/openAccess
OncodriveMUT
info:eu-repo/semantics/other
Software
Cancer driver mutations
TEXT
LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
11508
http://repositori.upf.edu/bitstream/10230/28131/3/LICENSE.txt.txt
b5a4c63e28b0a09a7fd4ec894f4e3cdf
MD5
3
ORIGINAL
oncodrivemut.zip
oncodrivemut.zip
application/octet-stream
43022
http://repositori.upf.edu/bitstream/10230/28131/1/oncodrivemut.zip
3e299fc12b2cb0eb858fe632ec442171
MD5
1
LICENSE.txt
LICENSE.txt
text/plain
11769
http://repositori.upf.edu/bitstream/10230/28131/2/LICENSE.txt
72fad9026bc80be88702bf077b104eff
MD5
2
10230/28131
oai:repositori.upf.edu:10230/28131
2017-03-18 03:33:04.05
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281332017-03-18T02:33:06Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Rodon, Jordi
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
2017-02-23T10:49:26Z
2017-02-23T10:49:26Z
2016-10
http://hdl.handle.net/10230/28133
Software: Anaconda Python 3.5
CGI drug prescription assigns targeted drugs to a tumor, based on its genomic alterations, according different levels of evidence (from pre-clinical assays to clinical guidelines).
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-23T10:49:26Z
No. of bitstreams: 1
tcgi-prescription-1.0.0.zip: 27226 bytes, checksum: febb99fbb1b935e2a0857794adb50d79 (MD5)
Made available in DSpace on 2017-02-23T10:49:26Z (GMT). No. of bitstreams: 1
tcgi-prescription-1.0.0.zip: 27226 bytes, checksum: febb99fbb1b935e2a0857794adb50d79 (MD5)
Previous issue date: 2016-10
eng
Universitat Pompeu Fabra
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document
http://bitbucket.org/intogen/intogen-pipeline/raw/a2569e57124108eabd6695009e8a6a682154e49e/LICENSE
info:eu-repo/semantics/openAccess
TCGI prescription
info:eu-repo/semantics/other
Software
Drug prescription
Personal medicine
TEXT
LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
11508
http://repositori.upf.edu/bitstream/10230/28133/3/LICENSE.txt.txt
b5a4c63e28b0a09a7fd4ec894f4e3cdf
MD5
3
ORIGINAL
tcgi-prescription-1.0.0.zip
tcgi-prescription-1.0.0.zip
application/octet-stream
27226
http://repositori.upf.edu/bitstream/10230/28133/1/tcgi-prescription-1.0.0.zip
febb99fbb1b935e2a0857794adb50d79
MD5
1
LICENSE.txt
LICENSE.txt
text/plain
11769
http://repositori.upf.edu/bitstream/10230/28133/2/LICENSE.txt
72fad9026bc80be88702bf077b104eff
MD5
2
10230/28133
oai:repositori.upf.edu:10230/28133
2017-03-18 03:33:06.424
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/281382017-03-18T02:33:03Zcom_10230_5963col_10230_24644
Tamborero Noguera, David
Rubio Pérez, Carlota
Déu Pons, Jordi
Schroeder, Michael Philipp, 1986-
Vivancos Prellezo, Ana
Rovira Guerín, Ana
Tusquets, Ignasi
Albanell Mestres, Joan
Tabernero Cartula, Josep
Dienstman, Rodrigo
González-Pérez, Abel
López Bigas, Núria
2017-02-24T11:40:49Z
2017-02-24T11:40:49Z
2016-10
http://hdl.handle.net/10230/28138
Collection of 28 tab-separated values (TSV) files.
This database contains the results of the driver analysis performed by the Cancer Genome Interpreter across 6,792 exomes of a pan-cancer cohort of 28 tumor types. Validated oncogenic mutations are identified according to the state-of-the-art clinical and experimental data, whereas the effect of the mutations of unknown significance is predicted by the OncodriveMUT method.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-02-24T11:40:49Z
No. of bitstreams: 1
intogen-driver-mutations.zip: 51147934 bytes, checksum: fa01f26acd5b49a799fb940aec825c29 (MD5)
Made available in DSpace on 2017-02-24T11:40:49Z (GMT). No. of bitstreams: 1
intogen-driver-mutations.zip: 51147934 bytes, checksum: fa01f26acd5b49a799fb940aec825c29 (MD5)
Previous issue date: 2016-10
eng
Universitat Pompeu Fabra
Més informació: IntOGen (web).
https://www.intogen.org/downloads
Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del document.
http://www.intogen.org/terms
info:eu-repo/semantics/openAccess
Intogen - Catalog of driver mutations
info:eu-repo/semantics/other
Dataset
Cancer genome driver
Oncogenic mutations
TEXT
LICENSE.txt.txt
LICENSE.txt.txt
Extracted text
text/plain
4062
http://repositori.upf.edu/bitstream/10230/28138/3/LICENSE.txt.txt
66869d16ea06ce0689b3a2735d1abb65
MD5
3
ORIGINAL
intogen-driver-mutations.zip
intogen-driver-mutations.zip
application/octet-stream
51147934
http://repositori.upf.edu/bitstream/10230/28138/1/intogen-driver-mutations.zip
fa01f26acd5b49a799fb940aec825c29
MD5
1
LICENSE.txt
LICENSE.txt
text/plain
4109
http://repositori.upf.edu/bitstream/10230/28138/2/LICENSE.txt
f3756c4538671a2402bdd6faa63dd896
MD5
2
10230/28138
oai:repositori.upf.edu:10230/28138
2017-03-18 03:33:03.745
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/282012021-12-22T07:54:40Zcom_10230_5963col_10230_34003col_10230_24644
Curto Tirado, Ariadna, 1987-
Donaire González, David
Barrera Gómez, Jose
Marshall, Julian D.
Nieuwenhuijsen, Mark J.
Wellenius, Gregory A.
Tonne, Cathryn
2017-03-10T09:22:48Z
2017-03-10T09:22:48Z
2016-02-22
http://hdl.handle.net/10230/28201
Sampling was conducted in a non-smoking private single-family house in the municipality of Terrassa (Spain) during February-March 2016.
There are 16 files of .txt format and 7 files of .csv format. The lightest file is 3KB and the heaviest 371KB. Counting all 23 files , there are 2,01MB.
Files from the HAPEX device are those which start with “HAPEX”. The following numbers correspond respectively to sensor ID_Day_Month_Year_Hour_Minute_Second of the sampling start.
Files from the TZOA-R device are those which start with “TZOA”. The following 4 digits correspond to the sensor ID.
Files from the DustTrak device are those which end with “dusttrak”. From 22 Feb to 25 Feb the number of the files’ name corresponds to DayMonthYear (DDMMYY) and HourMinute (HHMM) of the sampling start. In contrast, from 29 Feb, the number of the files’ name corresponds to DayMonthYear (DDMMYYYY) of the sampling start.
Files from the EL-USB-CO devices are those which end with “co”. From 22 Feb to 25 Feb the number of the files’ name corresponds to DayMonthYear (DDMMYYYY) of the sampling start plus DayMonthYear (DDMMYYYY) of the sampling end. The numbers before “co” correspond to the sensor ID (e.g. “1co”). In contrast, from 29 Feb, the number of the files’ name corresponds to DayMonthYear (DDMMYYYY) of the sampling start only.
File from the Q-Trak device is the one that ends with “qtrak”. The number of the files’ name corresponds to DayMonthYear (DDMMYYYY) of the sampling start.
File from BGI concentrations is the one that start with “BGI”. This is a database where the variable corresponding to the PM2.5 concentration is called “PMconcentration” (reported in µg/m3).
Raw data of PM2.5 and CO from an indoor wood-combustion experiment.
We evaluated the performance of two low-cost sensors measuring fine particulate matter (PM2.5) (HAPEX Nano, Climate Solutions Consulting, and TZOA-R Model RD02, MyTZOA) and one measuring carbon monoxide (CO) (EL-USB-CO, Lascar Electronics Ltd.) in a real-world wood-combustion experiment. PM2.5 devices were compared against a DustTrak (Model 8534, TSI Inc.) and a BGI pump (BGI4004, BGI Inc.) and the EL-USB-CO data-logger was compared against a Q-Trak (Model 7575, TSI Inc.). Sampling was conducted in a single-family house in Terrassa (Spain) during five non-consecutive days. All devices were co-located 1 meter away from an indoor fireplace and 0.6 meters above the ground. Fire was set once per day with hardwood logs and kept burning for 12 hours including a minimum of 2 hours with an opened window. The data provided is the raw output from all the devices tested for the 5 sampling days aiming interested researchers to play with the data and reproduce our findings.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2017-03-10T09:22:48Z
No. of bitstreams: 1
datasets.zip: 347522 bytes, checksum: 7a0f4448233cb80adbe08d1e6bc70b83 (MD5)
Made available in DSpace on 2017-03-10T09:22:48Z (GMT). No. of bitstreams: 1
datasets.zip: 347522 bytes, checksum: 7a0f4448233cb80adbe08d1e6bc70b83 (MD5)
Previous issue date: 2016-02-22
The research leading to these results received funding from the Brown India Initiative of Brown University and the European Research Council under ERC Grant Agreement number 336167 for the CHAI Project.
eng
Universitat Pompeu Fabra
Publicació relacionada: Curto A, Donaire-Gonzalez D, Barrera-Gómez J, Marshall JD, Nieuwenhuijsen MJ, Wellenius GA, Tonne C. Performance of low-cost monitors to assess household air pollution. Environ Res. 2018;163: 53-63. DOI: 10.1016/j.envres.2018.01.024 http://hdl.handle.net/10230/33850
http://hdl.handle.net/10230/33850
info:eu-repo/grantAgreement/EC/FP7/336167
Dades sota llicència Creative Commons Reconocimiento 3.0 España (CC BY 3.0 ES)
http://creativecommons.org/licenses/by/3.0/es/
info:eu-repo/semantics/openAccess
Performance of low-cost monitors to assess household air pollution [dataset]
info:eu-repo/semantics/other
Dataset
Indoor air pollution
Household air pollution
Low-cost sensors
Low-cost technology
Long-term sampling
HAPEX Nano
TZOA-R
DustTrak
EL-USB-CO
Q-Trak
ORIGINAL
datasets.zip
datasets.zip
application/octet-stream
347522
http://repositori.upf.edu/bitstream/10230/28201/1/datasets.zip
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MD5
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10230/28201
oai:repositori.upf.edu:10230/28201
2021-12-22 08:54:40.44
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/337432018-02-19T10:59:08Zcom_10230_5963col_10230_24644
Cirillo, Davide
2018-01-24T12:32:06Z
2018-01-24T12:32:06Z
2016
http://hdl.handle.net/10230/33743
Long noncoding RNAs (lncRNAs, which comprise 68% of the human transcriptome with average length of 1,000 nt) interact with various RNA-binding proteins (RBPs) to mediate cellular functions. Here we introduce Global Score as a tool to predict protein interactions with lncRNAs (http://service.tartaglialab.com/new_submission/globalscore). We used enhanced CLIP (eCLIP) to test the binding of the lncRNA Xist to the RBPs HnrnpK (Global Score of 0.99), Ptbp1 (0.99), Lbr (0.79), HnrnpU (Saf-A) (0.66), Spen (Sharp) (0.59) and negative control Dkc1 (0.01). Global Score prediction correlates with the eCLIP binding profile (Pearson correlation = 0.93). As for the binding sites, Spen and HnrnpK, Ptbp1, and Lbr interact respectively with Xist A, B, and E repeats and adjacent regions, while HnrnpU binds across the whole transcript, and Dkc1 does not interact with Xist.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2018-01-24T12:32:06Z
No. of bitstreams: 2
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Previous issue date: 2016
eng
Universitat Pompeu Fabra
Publicació relacionada: Cirillo, Davide. Prediction of protein and nucleic acid interactions. 2016. http://hdl.handle.net/10803/403537
http://hdl.handle.net/10803/403537
CC0 1.0 Universal
http://creativecommons.org/publicdomain/zero/1.0/
info:eu-repo/semantics/openAccess
Quantitative predictions of protein interactions with long noncoding RNAs
info:eu-repo/semantics/other
Dataset
CC-LICENSE
license_rdf
license_rdf
application/rdf+xml; charset=utf-8
1089
http://repositori.upf.edu/bitstream/10230/33743/2/license_rdf
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MD5
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ORIGINAL
Cirillo_quantitativePredictions_data.zip
Cirillo_quantitativePredictions_data.zip
application/octet-stream
2006516
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MD5
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10230/33743
oai:repositori.upf.edu:10230/33743
2018-02-19 11:59:08.719
Repositori digital de la UPF
repositori@upf.edu
oai:repositori.upf.edu:10230/345072018-04-28T01:30:12Zcom_10230_5963col_10230_24644
Dobon, Begoña
Hassan, Hisham Y.
Laayouni, Hafid, 1968-
Luisi, Pierre, 1985-
Ricaño Ponce, Isis
Zhernakova, Alexandra
Wijmenga, Cisca
Tahir, Hanan
Comas, David, 1969-
Netea, Mihai G
Bertranpetit, Jaume, 1952-
2018-04-27T09:42:54Z
2018-04-27T09:42:54Z
2018-04-27
http://hdl.handle.net/10230/34507
Includes Supplementary Figures S1-S13, Supplementary Tables S1-S8 and Supplementary Methods. Suppl. Fig. S1: Principal component analysis of the new populations genotyped from the Sudanese region; Suppl. Fig. S2: Principal component analysis of six world–wide populations from 1000 Genomes Project using different number of SNPs; Suppl. Fig. S3: Principal component analysis of the new populations genotyped from the Sudanese region; Suppl. Fig. S4: Principal component analysis of the populations from the Sudanese region in the context of the African continent with 14 samples identified as outliers with respect to their populations of origin; Suppl. Fig. S5: Pairwise FST values between the 14 populations; Suppl. Fig. S6: Cross-validation error estimates of the new nine genotyped populations for the ADMIXTURE analysis; Suppl. Fig. S7: ADMIXTURE results for k = 2 through k = 10 for the Sudanese populations; Suppl. Fig. S8: Cross-validation error estimates of the 14 populations for the ADMIXTURE analysis; Suppl. Fig. S9: ADMIXTURE results for k = 2 through k = 10 for the 14 populations using all 921 individuals; Suppl. Fig. S10: ADMIXTURE results for k = 2 through k = 10 for populations from the Sudanese region in the context of other external populations; Suppl. Fig. S11: Principal component analysis of the populations from the Sudanese region in the context of the African continent with an European population added; Suppl. Fig. S12: ADMIXTURE results for k = 2 through k = 10 for populations from the Sudanese region in the context of other external populations; Suppl. Fig. S13: Sampling distribution of the sample mean Global FST between Sudanese populations. Suppl. Table S1: Detailed sample information of the populations analysed in the present study, including sampling location and total number of individuals; Suppl. Table S2: Pairwise FST comparisons among the Sudanese ethnolinguistic groups and neighbouring populations; Suppl. Table S3: Three–population test with Yoruba as outgroup to estimate mixing proportions; Suppl. Table S4: Three–population test with Luya as outgroup to estimate mixing proportions; Suppl. Table S5: List of genes related to resistance to malaria present in the Immunochip; Suppl. Table S6: List of genes belonging to pathways related to antibacterial host defence present in the Immunochip; Suppl. Table S7: List of genes belonging to fungi host defence present in the Immunochip; Suppl. Table S8: Summary statistics of SNPs of disease-related genes from African populations of 1000 Genomes Project compared to the portion of those SNPs genotyped in the Immunochip. The compressed file contains the Sudan Inmunochip dataset in XLSX, BED, BIM and FAM formats.
Submitted by Dades de Recerca (repositori-becari3@upf.edu) on 2018-04-27T09:42:54Z
No. of bitstreams: 2
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Made available in DSpace on 2018-04-27T09:42:54Z (GMT). No. of bitstreams: 2
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SudanImmunochip.zip: 7343907 bytes, checksum: 0f8b630d314e7a699fb8819391c37541 (MD5)
application/pdf
eng
Universitat Pompeu Fabra
Publicació relacionada: Dobon B, Hassan HY, Laayouni H, Luisi P, Ricaño-Ponce I, Zhernakova A et al. The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape. Scientific Reports. 2015; 5: 9996. DOI 10.1038/srep09996 http://hdl.handle.net/10230/25768
http://hdl.handle.net/10230/25768
This work is licensed under a Creative Commons Attribution 4.0 International License.
http://creativecommons.org/licenses/by/4.0/
info:eu-repo/semantics/openAccess
The genetics of East African populations: a Nilo-Saharan component in the African genetic landscape [supplementary information]
info:eu-repo/semantics/other
THUMBNAIL
Dobon_SciRep_gene_suppl.pdf.jpg
Dobon_SciRep_gene_suppl.pdf.jpg
IM Thumbnail
image/jpeg
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TEXT
Dobon_SciRep_gene_suppl.pdf.txt
Dobon_SciRep_gene_suppl.pdf.txt
Extracted text
text/plain
37999
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ORIGINAL
Dobon_SciRep_gene_suppl.pdf
Dobon_SciRep_gene_suppl.pdf
Supplementary information
application/pdf
3480018
http://repositori.upf.edu/bitstream/10230/34507/2/Dobon_SciRep_gene_suppl.pdf
2b9e8fd3821bcd127a46ad44b7cf776c
MD5
2
SudanImmunochip.zip
SudanImmunochip.zip
Dataset
application/octet-stream
7343907
http://repositori.upf.edu/bitstream/10230/34507/3/SudanImmunochip.zip
0f8b630d314e7a699fb8819391c37541
MD5
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10230/34507
oai:repositori.upf.edu:10230/34507
2018-04-28 03:30:12.832
Repositori digital de la UPF
repositori@upf.edu