To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sRAP")
In most cases, you don't need to download the package archive at all.
sRAP
Simplified RNA-Seq Analysis Pipeline
Bioconductor version: 2.14
This package provides a pipeline for gene expression analysis (primarily for RNA-Seq data). The normalization function is specific for RNA-Seq analysis, but all other functions (Quality Control Figures, Differential Expression and Visualization, and Functional Enrichment via BD-Func) will work with any type of gene expression data.
Author: Charles Warden
Maintainer: Charles Warden <cwarden45 at gmail.com>
Citation (from within R,
enter citation("sRAP")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("sRAP")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("sRAP")
| R Script | sRAP Vignette | |
| Reference Manual |
Details
| biocViews | DifferentialExpression, GO, GeneExpression, GeneSetEnrichment, Microarray, Preprocessing, QualityControl, RNAseq, Software, Statistics, Visualization |
| Version | 1.4.2 |
| In Bioconductor since | BioC 2.13 (R-3.0) |
| License | GPL-3 |
| Depends | WriteXLS |
| Imports | gplots, pls, ROCR, qvalue |
| Suggests | |
| System Requirements | |
| URL | |
| Depends On Me | |
| Imports Me | |
| Suggests Me |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | sRAP_1.4.2.tar.gz |
| Windows Binary | sRAP_1.4.2.zip (32- & 64-bit) |
| Mac OS X 10.6 (Snow Leopard) | sRAP_1.4.2.tgz |
| Mac OS X 10.9 (Mavericks) | sRAP_1.4.2.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
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