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To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("compcodeR")
In most cases, you don't need to download the package archive at all.
compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: 3.1
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 <Charlotte.Soneson at isb-sib.ch>
Citation (from within R,
enter citation("compcodeR")):
Installation
To install this package, start R and enter:
## try http if https is not available
source("https://bioconductor.org/biocLite.R")
biocLite("compcodeR")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("compcodeR")
| R Script | compcodeR | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | DifferentialExpression, RNASeq, Software |
| Version | 1.4.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) (1.5 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 |
| LinkingTo | |
| Suggests | BiocStyle, EBSeq, DESeq, DESeq2(>= 1.1.31), baySeq(>= 1.16.0), genefilter, NOISeq, TCC, samr, NBPSeq |
| SystemRequirements | |
| Enhances | rpanel, DSS |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | compcodeR_1.4.0.tar.gz |
| Windows Binary | compcodeR_1.4.0.zip |
| Mac OS X 10.6 (Snow Leopard) | compcodeR_1.4.0.tgz |
| Mac OS X 10.9 (Mavericks) | compcodeR_1.4.0.tgz |
| Subversion source | (username/password: readonly) |
| Git source | https://github.com/Bioconductor-mirror/compcodeR/tree/release-3.1 |
| Package Short Url | http://bioconductor.org/packages/compcodeR/ |
| Package Downloads Report | Download Stats |
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