compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: 3.24 · Package version: 1.49.1
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("compcodeR")Details
| Maintainer | Charlotte Soneson <charlottesoneson@gmail.com> |
| Author | Charlotte Soneson [aut, cre] (ORCID: <https://orcid.org/0000-0003-3833-2169>), Paul Bastide [aut] (ORCID: <https://orcid.org/0000-0002-8084-9893>), Mélina Gallopin [aut] (ORCID: <https://orcid.org/0000-0002-2431-7825>) |
| License | GPL (>= 2) |
| URL | https://github.com/csoneson/compcodeR |
| Bug Reports | https://github.com/csoneson/compcodeR/issues |
| Source branch | devel |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, Software |
| Package Short Url | https://bioconductor.org/packages/compcodeR/ |
Citation
From within R, enter citation("compcodeR"):
Charlotte Soneson, Paul Bastide, Mélina Gallopin. compcodeR: RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods. doi:10.18129/B9.bioc.compcodeR, R package version 1.49.1, https://bioconductor.org/packages/compcodeR.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
- Comparing methods for differential expression analysis of RNAseq data with the compcodeR package
- Including inter-species measurements in differential expression analysis of RNAseq data with the compcodeR package
Download
Follow the installation instructions to use this package in your R session.
| Source package | compcodeR_1.49.1.tar.gz |
| Windows binary (x86_64) | compcodeR_1.49.1.zip |
| macOS binary (arm64) | compcodeR_1.49.1.tgz |
| macOS binary (x86_64) | compcodeR_1.49.1.tgz |
Dependencies
Depends: R (>= 4.0), sm
Imports: knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, caTools, grid, KernSmooth, MASS, ggplot2, stringr, statip, edgeR, limma, vioplot, methods, stats, utils, ape, phylolm, matrixStats, grDevices, graphics, rmarkdown, shiny, shinydashboard
Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk