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biocLite("compcodeR")
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compcodeR
RNAseq data simulation, differential expression analysis and performance comparison of differential expression methods
Bioconductor version: 3.0
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 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:
source("http://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 | 1.2.1 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| 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, DSS, TCC, samr, NBPSeq |
| SystemRequirements | |
| Enhances | rpanel |
| 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_1.2.1.tar.gz |
| Windows Binary | compcodeR_1.2.1.zip |
| Mac OS X 10.6 (Snow Leopard) | compcodeR_1.2.1.tgz |
| Mac OS X 10.9 (Mavericks) | compcodeR_1.2.1.tgz |
| Browse/checkout source | (username/password: readonly) |
| Package Downloads Report | Download Stats |
Common Bioconductor workflows include:
- Oligonucleotide Arrays
- High-throughput Sequencing
- Counting Reads for Differential Expression (parathyroideSE vignette)
- Annotation
- Annotating Variants
- Annotating Ranges
- Flow Cytometry and other assays
- Candidate Binding Sites for Known Transcription Factors
- Cloud-enabled cis-eQTL search and annotation
- RNA-Seq workflow: gene-level exploratory analysis and differential expression
- Changing genomic coordinate systems with rtracklayer::liftOver
- Mass spectrometry and proteomics data analysis
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