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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "transcriptR" in publications use:'
type: software
license: GPL-3.0-only
title: 'transcriptR: An Integrative Tool for ChIP- And RNA-Seq Based Primary Transcripts
  Detection and Quantification'
version: 1.40.0
doi: 10.32614/CRAN.package.transcriptR
abstract: 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.
authors:
- family-names: Karapetyan
  given-names: Armen R.
  email: armen.karapetyan87@gmail.com
repository: https://bioc-release.r-universe.dev
commit: d11889d3cfb1fb048ad7652a2648cb4691ebb65b
date-released: '2021-11-20'
contact:
- family-names: Karapetyan
  given-names: Armen R.
  email: armen.karapetyan87@gmail.com