compcodeR
This package is for version 3.7 of Bioconductor; for the stable, up-to-date release version, see compcodeR.
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: 3.7
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 and interfaces to several packages for performing the differential expression analysis.
Author: Charlotte Soneson
Maintainer: Charlotte Soneson <charlottesoneson at gmail.com>
citation("compcodeR")):
Installation
To install this package, start R (version "3.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
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 | R Script | |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, RNASeq, Software |
| Version | 1.16.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) (10 years) |
| License | GPL (>= 2) |
| Depends | R (>= 3.0.2), sm |
| Imports | tcltk, knitr (>= 1.2), markdown, ROCR, lattice (>= 0.16), gplots, gtools, gdata, caTools, grid, KernSmooth, MASS, ggplot2, stringr, modeest, edgeR, limma, vioplot, methods |
| System Requirements | |
| URL |
See More
| Suggests | BiocStyle, EBSeq, DESeq, DESeq2(>= 1.1.31), baySeq(>= 2.2.0), genefilter, NOISeq, TCC, NBPSeq (>= 0.3.0) |
| 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_1.16.1.tar.gz |
| Windows Binary | compcodeR_1.16.1.zip |
| Mac OS X 10.11 (El Capitan) | compcodeR_1.16.1.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 |
| Old Source Packages for BioC 3.7 | Source Archive |