depmap

DOI: 10.18129/B9.bioc.depmap  

Cancer Dependency Map Data Package

Bioconductor version: Release (3.16)

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. The 19Q3 release adds the drug_dependency dataset, that contains cancer cell line dependency data with respect to drug and drug-candidate compounds. The 20Q2 release adds the proteomic dataset that contains quantitative profiling of proteins via mass spectrometry. 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>

Installation

To install this package, start R (version "4.2") and enter:

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

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	1.12.0
License	Artistic-2.0
Depends	R (>= 3.6), methods, dplyr
Imports	utils, ExperimentHub, AnnotationHub
LinkingTo
Suggests	knitr, rmarkdown, BiocStyle, viridis, gridExtra, ggplot2, readr, tibble, stringr, tidyr
SystemRequirements
Enhances
URL
Depends On Me
Imports Me	MAGeCKFlute
Suggests Me	BioPlex
Links To Me
Build Report

Package Archives

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

Source Package	depmap_1.12.0.tar.gz
Windows Binary
macOS Binary (x86_64)
macOS Binary (arm64)
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	https://bioconductor.org/packages/depmap/
Package Downloads Report	Download Stats