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transcriptR

This is the development version of transcriptR; for the stable release version, see transcriptR.

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


Bioconductor version: Development (3.19)

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 (version "4.4") and enter:


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

# The following initializes usage of Bioc devel
BiocManager::install(version='devel')

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

Details

biocViews Coverage, ImmunoOncology, RNASeq, Sequencing, Software, Transcription
Version 1.31.0
In Bioconductor since BioC 3.3 (R-3.3) (8 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
System Requirements
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Suggests BiocStyle, knitr, rmarkdown, TxDb.Hsapiens.UCSC.hg19.knownGene, testthat
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Package Archives

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

Source Package transcriptR_1.31.0.tar.gz
Windows Binary transcriptR_1.31.0.zip
macOS Binary (x86_64) transcriptR_1.31.0.tgz
macOS Binary (arm64) transcriptR_1.31.0.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/
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