- Home
- Bioconductor 3.0
- Software Packages
- easyRNASeq
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")
In most cases, you don't need to download the package archive at all.
easyRNASeq
Count summarization and normalization for RNA-Seq data.
Bioconductor version: 3.0
Calculates the coverage of high-throughput short-reads against a genome of reference and summarizes it per feature of interest (e.g. exon, gene, transcript). The data can be normalized as 'RPKM' or by the 'DESeq' or 'edgeR' package.
Author: Nicolas Delhomme, Ismael Padioleau, Bastian Schiffthaler
Maintainer: Nicolas Delhomme <delhomme at embl.de>
Citation (from within R,
enter citation("easyRNASeq")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("easyRNASeq")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("easyRNASeq")
| R Script | easyRNASeq | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | GeneExpression, Genetics, Preprocessing, RNASeq, Software |
| Version | 2.2.1 |
| In Bioconductor since | BioC 2.10 (R-2.15) |
| License | Artistic-2.0 |
| Depends | |
| Imports | Biobase(>= 2.26.0), BiocGenerics(>= 0.12.1), biomaRt(>= 2.22.0), Biostrings(>= 2.34.1), DESeq(>= 1.18.0), edgeR(>= 3.8.5), genomeIntervals(>= 1.22.0), GenomicAlignments(>= 1.2.1), GenomeInfoDb(>= 1.2.4), GenomicRanges(>= 1.18.4), graphics, IRanges(>= 2.0.1), LSD (>= 3.0), methods, parallel, Rsamtools(>= 1.18.2), S4Vectors(>= 0.4.0), ShortRead(>= 1.24.0), utils |
| LinkingTo | |
| Suggests | BiocStyle(>= 1.4.1), BSgenome(>= 1.34.1), BSgenome.Dmelanogaster.UCSC.dm3(>= 1.4.0), GenomicFeatures(>= 1.18.3), RnaSeqTutorial(>= 0.3.1), RUnit (>= 0.4.28) |
| SystemRequirements | |
| Enhances | |
| URL | |
| Depends On Me | RnaSeqTutorial |
| Imports Me | |
| Suggests Me | SeqGSEA |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | easyRNASeq_2.2.1.tar.gz |
| Windows Binary | easyRNASeq_2.2.1.zip |
| Mac OS X 10.6 (Snow Leopard) | easyRNASeq_2.2.1.tgz |
| Mac OS X 10.9 (Mavericks) | easyRNASeq_2.2.1.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
Post questions about Bioconductor packages to our mailing lists. Read the posting guide before posting!
Contact us: support.bioconductor.org
Hosting provided by Fred Hutchinson Cancer Research Center
Copyright © 2003 - 2015, Bioconductor
