compcodeR
This is the development version of compcodeR; for the stable release version, see compcodeR.
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: Development (3.24)
This package provides extensive functionality for comparing results obtained by different methods for differential expression analysis of RNAseq data. It also contains functions for simulating count data. Finally, it provides convenient interfaces to several packages for performing the differential expression analysis. These can also be used as templates for setting up and running a user-defined differential analysis workflow within the framework of the package.
Author: Charlotte Soneson [aut, cre]
, Paul Bastide [aut]
, Mélina Gallopin [aut]
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
citation("compcodeR")):
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")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("compcodeR")
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("compcodeR")| compcodeR | HTML | R Script |
| phylocompcodeR | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, Software |
| Version | 1.49.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (12.5 years) |
| License | GPL (>= 2) |
| Depends | R (>= 4.0), sm |
| Imports | knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard |
| System Requirements | |
| URL | https://github.com/csoneson/compcodeR |
| Bug Reports | https://github.com/csoneson/compcodeR/issues |
See More
| Suggests | BiocStyle, EBSeq, DESeq2(>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk |
| Linking To | |
| Enhances | rpanel, DSS |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | compcodeR_1.49.0.tar.gz |
| Windows Binary (x86_64) | compcodeR_1.49.0.zip |
| macOS Binary (big-sur-x86_64) | compcodeR_1.49.0.tgz |
| macOS Binary (sonoma-arm64) | compcodeR_1.49.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/compcodeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/compcodeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/compcodeR/ |
| Package Short Url | https://bioconductor.org/packages/compcodeR/ |
| Package Downloads Report | Download Stats |