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

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>
Date of publicationNone
MaintainerArmen R. Karapetyan <armen.karapetyan87@gmail.com>
LicenseGPL-3
Version1.2.0

View on Bioconductor

Functions

addFeature Man page
addFeature,ChipDataSet-method Man page
annot Man page
annotateTranscripts Man page
annotateTranscripts,TranscriptionDataSet,GRanges-method Man page
breakTranscriptsByPeaks Man page
breakTranscriptsByPeaks,TranscriptionDataSet,ChipDataSet-method Man page
cds Man page
ChipDataSet Man page
ChipDataSet-class Man page
constructCDS Man page
constructTDS Man page
detectTranscripts Man page
detectTranscripts,TranscriptionDataSet-method Man page
estimateBackground Man page
estimateBackground,TranscriptionDataSet-method Man page
estimateGapDistance Man page
estimateGapDistance,TranscriptionDataSet,GRanges-method Man page
exportCoverage Man page
exportCoverage,TranscriptionDataSet-method Man page
getConfusionMatrix Man page
getConfusionMatrix,ChipDataSet-method Man page
getGenomicAnnot Man page
getGenomicAnnot,ChipDataSet-method Man page
getPeaks Man page
getPeaks,ChipDataSet-method Man page
getPredictorSignificance Man page
getPredictorSignificance,ChipDataSet-method Man page
getProbTreshold Man page
getProbTreshold,ChipDataSet-method Man page
getQuadProb Man page
getQuadProb,ChipDataSet-method Man page
getTestedGapDistances Man page
getTestedGapDistances,TranscriptionDataSet-method Man page
getTranscripts Man page
getTranscripts,TranscriptionDataSet-method Man page
peaksToBed Man page
peaksToBed,ChipDataSet-method Man page
plotErrorRate Man page
plotErrorRate,TranscriptionDataSet-method Man page
plotFeatures Man page
plotFeatures,ChipDataSet-method Man page
plotGenomicAnnot Man page
plotGenomicAnnot,ChipDataSet-method Man page
plotROC Man page
plotROC,ChipDataSet-method Man page
predictStrand Man page
predictStrand,ChipDataSet,TranscriptionDataSet-method Man page
predictTssOverlap Man page
predictTssOverlap,ChipDataSet-method Man page
show Man page
show,ChipDataSet-method Man page
show,TranscriptionDataSet-method Man page
tds Man page
TranscriptionDataSet Man page
TranscriptionDataSet-class Man page
transcriptsToBed Man page
transcriptsToBed,GRanges-method Man page

Files

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

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