transcriptR

DOI: 10.18129/B9.bioc.transcriptR  

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

Bioconductor version: Release (3.16)

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>

Installation

To install this package, start R (version "4.2") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("transcriptR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

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

browseVignettes("transcriptR")

 

HTML	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, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version	1.26.0
In Bioconductor since	BioC 3.3 (R-3.3) (7 years)
License	GPL-3
Depends	R (>= 3.5.0), methods
Imports	BiocGenerics, caret, chipseq, e1071, GenomicAlignments, GenomicRanges, GenomicFeatures, GenomeInfoDb, ggplot2, graphics, grDevices, IRanges(>= 2.11.15), 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
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Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	transcriptR_1.26.0.tar.gz
Windows Binary	transcriptR_1.26.0.zip
macOS Binary (x86_64)	transcriptR_1.26.0.tgz
macOS Binary (arm64)	transcriptR_1.26.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/transcriptR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/transcriptR
Bioc Package Browser	https://code.bioconductor.org/browse/transcriptR/
Package Short Url	https://bioconductor.org/packages/transcriptR/
Package Downloads Report	Download Stats