OncodriveMUT

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• dc.contributor.author Tamborero Noguera, Davidca
• dc.contributor.author Rubio Pérez, Carlotaca
• dc.contributor.author Déu Pons, Jordica
• dc.contributor.author Schroeder, Michael Philipp, 1986-ca
• dc.contributor.author Vivancos Prellezo, Anaca
• dc.contributor.author Rovira Guerín, Anaca
• dc.contributor.author Tusquets, Ignasica
• dc.contributor.author Albanell Mestres, Joanca
• dc.contributor.author Rodon, Jordica
• dc.contributor.author Tabernero Cartula, Josepca
• dc.contributor.author Dienstman, Rodrigoca
• dc.contributor.author González-Pérez, Abelca
• dc.contributor.author López Bigas, Núriaca
• dc.date.accessioned 2017-02-22T12:41:22Z
• dc.date.available 2017-02-22T12:41:22Z
• dc.date.issued 2016-01
• dc.description 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 mutationsca
• dc.description.abstract Bioinformatics method to identify individual driver mutations.ca
• dc.identifier.doi https://doi.org/10.34810/data432
• dc.identifier.uri http://hdl.handle.net/10230/28131
• dc.language.iso engca
• dc.publisher Universitat Pompeu Fabraca
• dc.rights Universitat Pomper Fabra License Agreement. Consulteu les condicions d'ús específiques dins del documentca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.rights.uri http://bitbucket.org/intogen/intogen-pipeline/raw/a2569e57124108eabd6695009e8a6a682154e49e/LICENSE
• dc.subject.keyword Cancer driver mutations
• dc.title OncodriveMUTca
• dc.type info:eu-repo/semantics/otherca
• dc.type Software