OncodriveFM

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• dc.contributor.author González-Pérez, Abelca
• dc.contributor.author López Bigas, Núriaca
• dc.date.accessioned 2017-01-26T10:45:34Z
• dc.date.available 2017-01-26T10:45:34Z
• dc.date.issued 2015-10
• dc.description 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 notsetca
• dc.description.abstract 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.ca
• dc.identifier.doi https://doi.org/10.34810/data413
• dc.identifier.uri http://hdl.handle.net/10230/27994
• dc.language.iso engca
• dc.publisher Universitat Pompeu Fabraca
• dc.relation 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
• dc.relation Més informació: OncodriveFM (Bitbucket)
• dc.relation.isreferencedby http://hdl.handle.net/10230/23344
• dc.relation.uri https://bitbucket.org/bbglab/oncodrivefm
• dc.rights Universitat Pompeu Fabra Free Source Code License Agreement. Consulteu les condicions d'ús específiques dins del document.ca
• dc.rights.accessRights info:eu-repo/semantics/openAccessca
• dc.subject.keyword Cancer
• dc.subject.keyword Genes
• dc.subject.keyword Driver
• dc.subject.keyword Functional mutations
• dc.title OncodriveFMca
• dc.type info:eu-repo/semantics/otherca
• dc.type Software