BloodCancerMultiOmics2017
This is the released version of BloodCancerMultiOmics2017; for the devel version, see BloodCancerMultiOmics2017.
"Drug-perturbation-based stratification of blood cancer" by Dietrich S, Oleś M, Lu J et al. - experimental data and complete analysis
Bioconductor version: Release (3.23)
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, Oleś M, Lu J et al., J. Clin. Invest. (2018) 128(1):427-445. doi:10.1172/JCI93801.
Author: Małgorzata Oleś, Sascha Dietrich, Junyan Lu, Britta Velten, Andreas Mock, Vladislav Kim, Wolfgang Huber
Maintainer: Małgorzata Oleś <dr.malgorzata.oles at gmail.com>
citation("BloodCancerMultiOmics2017")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("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")| BloodCancerMultiOmics2017 | HTML | R Script |
| BloodCancerMultiOmics2017 - data overview | HTML | R Script |
| Reference Manual |
Details
| biocViews | CancerData, ExperimentData, LeukemiaCancerData, ReproducibleResearch |
| Version | 1.32.0 |
| 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 |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, knitr, rmarkdown, abind, AnnotationDbi, biomaRt, broom, colorspace, cowplot, dendsort, doParallel, foreach, forestplot, genefilter, ggbeeswarm, ggtern, gridExtra, hexbin, limma, magrittr, Matrix, maxstat, nat, org.Hs.eg.db, pheatmap, piano, readxl, Rtsne, tidyr, xtable |
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| Depends On Me | |
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| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | BloodCancerMultiOmics2017_1.32.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (big-sur-x86_64) | |
| macOS Binary (sonoma-arm64) | |
| 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 |