To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("roar")
In most cases, you don't need to download the package archive at all.
roar
Identify differential APA usage from RNA-seq alignments
Bioconductor version: 3.0
Identify preferential usage of APA sites, comparing two biological conditions, starting from known alternative sites and alignments obtained from standard RNA-seq experiments.
Author: Elena Grassi
Maintainer: Elena Grassi <grassi.e at gmail.com>
Citation (from within R,
enter citation("roar")):
Installation
To install this package, start R and enter:
source("http://bioconductor.org/biocLite.R")
biocLite("roar")
Documentation
To view documentation for the version of this package installed in your system, start R and enter:
browseVignettes("roar")
| R Script | Identify differential APA usage from RNA-seq alignments | |
| Reference Manual | ||
| Text | NEWS |
Details
| biocViews | HighThroughputSequencing, RNAseq, Sequencing, Software, Transcription |
| Version | 1.2.0 |
| In Bioconductor since | BioC 2.14 (R-3.1) |
| License | GPL-3 |
| Depends | R (>= 3.0.1) |
| Imports | GenomicRanges, GenomicAlignments(>= 0.99.4), methods, rtracklayer, S4Vectors |
| LinkingTo | |
| Suggests | RUnit, BiocGenerics, RNAseqData.HNRNPC.bam.chr14 |
| SystemRequirements | |
| Enhances | |
| URL | https://github.com/vodkatad/roar/ |
| Depends On Me | |
| Imports Me | |
| Suggests Me | |
| Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Package Source | roar_1.2.0.tar.gz |
| Windows Binary | roar_1.2.0.zip |
| Mac OS X 10.6 (Snow Leopard) | roar_1.2.0.tgz |
| Mac OS X 10.9 (Mavericks) | roar_1.2.0.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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