transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts Detection and Quantification
Version 1.4.0

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.

AuthorArmen R. Karapetyan <armen.karapetyan87@gmail.com>
Bioconductor views Coverage RNASeq Sequencing Software Transcription
Date of publicationNone
MaintainerArmen R. Karapetyan <armen.karapetyan87@gmail.com>
LicenseGPL-3
Version1.4.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("transcriptR")

Getting started

transcriptR: an integrative tool for ChIP- and RNA-seq based primary transcripts detection and quantification

Popular man pages

annotateTranscripts-methods: annotateTranscripts
constructCDS: constructCDS
estimateBackground-methods: estimateBackground
plotFeatures-methods: plotFeatures
predictStrand-methods: predictStrand
show: Show method for ChipDataSet and TranscriptionDataSet objects
transcriptsToBed-methods: transcriptsToBed
See all...

All man pages Function index File listing

Man pages

addFeature-methods: addFeature
annot: Reference annotation (knownGene from UCSC)
annotateTranscripts-methods: annotateTranscripts
breakTranscriptsByPeaks-methods: breakTranscriptsByPeaks
cds: Example of 'ChipDataSet' object.
ChipDataSet-class: ChipDataSet
constructCDS: constructCDS
constructTDS: constructTDS
detectTranscripts-methods: detectTranscripts
estimateBackground-methods: estimateBackground
estimateGapDistance-methods: estimateGapDistance
exportCoverage-methods: exportCoverage
getConfusionMatrix-methods: getConfusionMatrix
getGenomicAnnot-methods: getGenomicAnnot
getPeaks-methods: getPeaks
getPredictorSignificance-methods: getPredictorSignificance
getProbTreshold-methods: getProbTreshold
getQuadProb-methods: getQuadProb
getTestedGapDistances-methods: getTestedGapDistances
getTranscripts-methods: getTranscripts
peaksToBed-methods: peaksToBed
plotErrorRate-methods: plotErrorRate
plotFeatures-methods: plotFeatures
plotGenomicAnnot-methods: plotGenomicAnnot
plotROC-methods: plotROC
predictStrand-methods: predictStrand
predictTssOverlap-methods: predictTssOverlap
show: Show method for ChipDataSet and TranscriptionDataSet objects
tds: Example of 'TranscriptionDataSet' object.
TranscriptionDataSet-class: TranscriptionDataSet
transcriptsToBed-methods: transcriptsToBed

Functions

Files

DESCRIPTION
NAMESPACE
NEWS
R
R/ChipDataSet-class.R
R/ChipDataSet-generics.R
R/ChipDataSet-methods.R
R/TranscriptionDataSet-class.R
R/TranscriptionDataSet-generics.R
R/TranscriptionDataSet-methods.R
R/show.R
R/utils.R
build
build/vignette.rds
data
data/annot.rda
data/cds.rda
data/datalist
data/tds.rda
inst
inst/doc
inst/doc/transcriptR.R
inst/doc/transcriptR.Rmd
inst/doc/transcriptR.pdf
inst/extdata
inst/extdata/chip_reads.bam
inst/extdata/chip_reads.bam.bai
inst/extdata/peaks.txt
inst/extdata/rna_reads.bam
inst/extdata/rna_reads.bam.bai
man
man/ChipDataSet-class.Rd
man/TranscriptionDataSet-class.Rd
man/addFeature-methods.Rd
man/annot.Rd
man/annotateTranscripts-methods.Rd
man/breakTranscriptsByPeaks-methods.Rd
man/cds.Rd
man/constructCDS.Rd
man/constructTDS.Rd
man/detectTranscripts-methods.Rd
man/estimateBackground-methods.Rd
man/estimateGapDistance-methods.Rd
man/exportCoverage-methods.Rd
man/getConfusionMatrix-methods.Rd
man/getGenomicAnnot-methods.Rd
man/getPeaks-methods.Rd
man/getPredictorSignificance-methods.Rd
man/getProbTreshold-methods.Rd
man/getQuadProb-methods.Rd
man/getTestedGapDistances-methods.Rd
man/getTranscripts-methods.Rd
man/peaksToBed-methods.Rd
man/plotErrorRate-methods.Rd
man/plotFeatures-methods.Rd
man/plotGenomicAnnot-methods.Rd
man/plotROC-methods.Rd
man/predictStrand-methods.Rd
man/predictTssOverlap-methods.Rd
man/show.Rd
man/tds.Rd
man/transcriptsToBed-methods.Rd
tests
tests/testthat
tests/testthat.R
tests/testthat/test-ChipDataSet-methods.R
tests/testthat/test-TranscriptionDataSet-methods.R
tests/testthat/test-objects.R
vignettes
vignettes/images
vignettes/images/Average_RNAseq_signal_across_peak_region.png
vignettes/images/Gene_associated_peak_prediction.png
vignettes/images/Main_scheme.png
vignettes/images/Peak_strandedness_prediction.png
vignettes/transcriptR.Rmd
vignettes/transcriptR.bib
transcriptR documentation built on May 20, 2017, 9:29 p.m.

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