depmap

DOI: 10.18129/B9.bioc.depmap    

This is the development version of depmap; to use it, please install the devel version of Bioconductor.

Cancer Dependency Map Data Package

Bioconductor version: Development (3.10)

The depmap package is a data package that accesses datsets from the Broad Institute DepMap cancer dependency study using ExperimentHub. Datasets from the most current release are available, including RNAI and CRISPR-Cas9 gene knockout screens quantifying the genetic dependency for select cancer cell lines. Additional datasets are also available pertaining to the log copy number of genes for select cell lines, protein expression of cell lines as measured by reverse phase protein lysate microarray (RPPA), 'Transcript Per Million' (TPM) data, as well as supplementary datasets which contain metadata and mutation calls for the other datasets found in the current release. This package will be updated on a quarterly basis to incorporate the latest Broad Institute DepMap Public cancer dependency datasets. All data made available in this package was generated by the Broad Institute DepMap for research purposes and not intended for clinical use. This data is distributed under the Creative Commons license (Attribution 4.0 International (CC BY 4.0)).

Author: Laurent Gatto [cre, aut], Theo Killian [aut]

Maintainer: Laurent Gatto <laurent.gatto at uclouvain.be>

Citation (from within R, enter citation("depmap")):

Installation

To install this package, start R (version "3.6") and enter:

if (!requireNamespace("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

BiocManager::install("depmap")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("depmap")

 

HTML R Script depmap
HTML R Script depmap use cases
PDF   Reference Manual
Text   NEWS

Details

biocViews AssayDomainData, BreastCancerData, CancerData, CellCulture, ColonCancerData, CopyNumberVariationData, DiseaseModel, ExperimentData, ExperimentHub, Genome, Homo_sapiens_Data, KidneyCancerData, LeukemiaCancerData, LungCancerData, OrganismData, OvarianCancerData, PackageTypeData, ProstateCancerData, Proteome, RepositoryData, ReproducibleResearch, SpecimenSource, StemCell, Tissue
Version 0.99.5
License Artistic-2.0
Depends R (>= 3.6), methods, dplyr, ExperimentHub
Imports utils
LinkingTo
Suggests knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report  

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package depmap_0.99.5.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository git clone https://git.bioconductor.org/packages/depmap
Source Repository (Developer Access) git clone git@git.bioconductor.org:packages/depmap
Package Short Url http://bioconductor.org/packages/depmap/
Package Downloads Report Download Stats

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