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# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
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cff-version: 1.2.0
message: 'To cite package "proActiv" in publications use:'
type: software
license: MIT
title: 'proActiv: Estimate Promoter Activity from RNA-Seq data'
version: 1.15.0
doi: 10.1016/j.cell.2019.08.018
abstract: Most human genes have multiple promoters that control the expression of
  different isoforms. The use of these alternative promoters enables the regulation
  of isoform expression pre-transcriptionally. Alternative promoters have been found
  to be important in a wide number of cell types and diseases. proActiv is an R package
  that enables the analysis of promoters from RNA-seq data. proActiv uses aligned
  reads as input, and generates counts and normalized promoter activity estimates
  for each annotated promoter. In particular, proActiv accepts junction files from
  TopHat2 or STAR or BAM files as inputs. These estimates can then be used to identify
  which promoter is active, which promoter is inactive, and which promoters change
  their activity across conditions. proActiv also allows visualization of promoter
  activity across conditions.
authors:
- family-names: Demircioglu
  given-names: Deniz
  email: ddemircioglu@gis.a-star.edu.sg
  orcid: https://orcid.org/0000-0001-7857-0407
- family-names: Göke
  given-names: Jonathan
  email: gokej@gis.a-star.edu.sg
- family-names: Lee
  given-names: Joseph
  email: joseph.lee@u.nus.edu
preferred-citation:
  type: article
  title: A Pan-cancer Transcriptome Analysis Reveals Pervasive Regulation through
    Alternative Promoters
  authors:
  - family-names: Demircioglu
    given-names: Deniz
    email: ddemircioglu@gis.a-star.edu.sg
    orcid: https://orcid.org/0000-0001-7857-0407
  - family-names: Cukuroglu
    given-names: Engin
  - family-names: Kindermans
    given-names: Martin
  - family-names: Nandi
    given-names: Tannistha
  - family-names: Calabrese
    given-names: Claudia
  - family-names: Fonseca
    given-names: Nuno A.
  - family-names: Kahles
    given-names: Andre
  - family-names: Lehmann
    given-names: Kjong-Van
  - family-names: Stegle
    given-names: Oliver
  - family-names: Brazma
    given-names: Alvis
  - family-names: Brooks
    given-names: Angela N.
  - family-names: Ratsch
    given-names: Gunnar
  - family-names: Tan
    given-names: Patrick
  - family-names: Goke
    given-names: Jonathan
  year: '2019'
  journal: Cell
  doi: 10.1016/j.cell.2019.08.018
  volume: '178'
  issue: '6'
  start: '1465'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/GoekeLab/proActiv
url: https://github.com/GoekeLab/proActiv
contact:
- family-names: Lee
  given-names: Joseph
  email: joseph.lee@u.nus.edu