BloodCancerMultiOmics2017

DOI: 10.18129/B9.bioc.BloodCancerMultiOmics2017    

This package is for version 3.9 of Bioconductor; for the stable, up-to-date release version, see BloodCancerMultiOmics2017.

"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al. - experimental data and complete analysis

Bioconductor version: 3.9

The package contains data of the Primary Blood Cancer Encyclopedia (PACE) project together with a complete executable transcript of the statistical analysis and reproduces figures presented in the paper "Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oles M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.

Author: Malgorzata Oles, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber

Maintainer: Malgorzata Oles <malgorzata.oles at embl.de>

Installation

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

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

BiocManager::install("BloodCancerMultiOmics2017")

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("BloodCancerMultiOmics2017")

 

HTML	R Script	BloodCancerMultiOmics2017
HTML	R Script	BloodCancerMultiOmics2017 - data overview
PDF		Reference Manual

Details

biocViews	CancerData, ExperimentData, LeukemiaCancerData, ReproducibleResearch
Version	1.4.0
License	LGPL (>= 3)
Depends	R (>= 3.5.0)
Imports	beeswarm, Biobase, DESeq2, devtools, dplyr, ggdendro, ggplot2, glmnet, graphics, grDevices, grid, gtable, ipflasso, methods, RColorBrewer, reshape2, scales, stats, SummarizedExperiment, survival, tibble
LinkingTo
Suggests	BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, IHW, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, tidyverse, xtable
SystemRequirements
Enhances
URL
Depends On Me
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Suggests Me
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Build Report

Package Archives

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

Source Package	BloodCancerMultiOmics2017_1.4.0.tar.gz
Windows Binary
Mac OS X 10.11 (El Capitan)
Source Repository	git clone https://git.bioconductor.org/packages/BloodCancerMultiOmics2017
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/BloodCancerMultiOmics2017
Package Short Url	https://bioconductor.org/packages/BloodCancerMultiOmics2017/
Package Downloads Report	Download Stats