compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: 3.23 · Package version: 1.48.0
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 |
| Downloads rank | 534 |
| Source branch | RELEASE_3_23 |
| biocViews | DifferentialExpression, ImmunoOncology, RNASeq, Software |
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
Dependencies
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
Suggests: BiocStyle, EBSeq, DESeq2 (>= 1.1.31), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0), phytools, phangorn, testthat, ggtree, tidytree, statmod, covr, sva, tcltk