To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("transcriptR")

In most cases, you don't need to download the package archive at all.

transcriptR

 

   

An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification

Bioconductor version: Release (3.5)

The differences in the RNA types being sequenced have an impact on the resulting sequencing profiles. mRNA-seq data is enriched with reads derived from exons, while GRO-, nucRNA- and chrRNA-seq demonstrate a substantial broader coverage of both exonic and intronic regions. The presence of intronic reads in GRO-seq type of data makes it possible to use it to computationally identify and quantify all de novo continuous regions of transcription distributed across the genome. This type of data, however, is more challenging to interpret and less common practice compared to mRNA-seq. One of the challenges for primary transcript detection concerns the simultaneous transcription of closely spaced genes, which needs to be properly divided into individually transcribed units. The R package transcriptR combines RNA-seq data with ChIP-seq data of histone modifications that mark active Transcription Start Sites (TSSs), such as, H3K4me3 or H3K9/14Ac to overcome this challenge. The advantage of this approach over the use of, for example, gene annotations is that this approach is data driven and therefore able to deal also with novel and case specific events. Furthermore, the integration of ChIP- and RNA-seq data allows the identification all known and novel active transcription start sites within a given sample.

Author: Armen R. Karapetyan <armen.karapetyan87 at gmail.com>

Maintainer: Armen R. Karapetyan <armen.karapetyan87 at gmail.com>

Citation (from within R, enter citation("transcriptR")):

Installation

To install this package, start R and enter:

## try http:// if https:// URLs are not supported
source("https://bioconductor.org/biocLite.R")
biocLite("transcriptR")

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("transcriptR")

 

PDF R Script transcriptR: an integrative tool for ChIP- and RNA-seq based primary transcripts detection and quantification
PDF   Reference Manual
Text   NEWS

Details

biocViews Coverage, RNASeq, Sequencing, Software, Transcription
Version 1.4.0
In Bioconductor since BioC 3.3 (R-3.3) (1 year)
License GPL-3
Depends methods, R (>= 3.3)
Imports BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges, pROC, reshape2, Rsamtools, rtracklayer, S4Vectors, stats, utils
LinkingTo
Suggests BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
SystemRequirements
Enhances
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 transcriptR_1.4.0.tar.gz
Windows Binary transcriptR_1.4.0.zip
Mac OS X 10.11 (El Capitan) transcriptR_1.4.0.tgz
Subversion source (username/password: readonly)
Git source https://github.com/Bioconductor-mirror/transcriptR/tree/release-3.5
Package Short Url http://bioconductor.org/packages/transcriptR/
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