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Bioconductor - compcodeR (development version)

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 (3.22)

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] ORCID: 0000-0003-3833-2169 , Paul Bastide [aut] ORCID: 0000-0002-8084-9893 , Mélina Gallopin [aut] ORCID: 0000-0002-2431-7825

Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>

Citation (from within R, enter citation("compcodeR")): Installation

To install this package, start R (version "4.5") and enter:


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

# The following initializes usage of Bioc devel
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")
Details biocViews DifferentialExpression, ImmunoOncology, RNASeq, Software Version 1.45.0 In Bioconductor since BioC 2.14 (R-3.1) (11 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.

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