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.

Author
Armen R. Karapetyan <armen.karapetyan87@gmail.com>
Date of publication
None
Maintainer
Armen R. Karapetyan <armen.karapetyan87@gmail.com>
License
GPL-3
Version
1.2.0

View on Bioconductor

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

Files in this package

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