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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 "CAGEr" in publications use:'
type: software
license: GPL-3.0-only
title: 'CAGEr: Analysis of CAGE (Cap Analysis of Gene Expression) sequencing data
  for precise mapping of transcription start sites and promoterome mining'
version: 2.11.3
doi: 10.1093/nar/gkv054
abstract: The _CAGEr_ package identifies transcription start sites (TSS) and their
  usage frequency from CAGE (Cap Analysis Gene Expression) sequencing data. It normalises
  raw CAGE tag count, clusters TSSs into tag clusters (TC) and aggregates them across
  multiple CAGE experiments to construct consensus clusters (CC) representing the
  promoterome. CAGEr provides functions to profile expression levels of these clusters
  by cumulative expression and rarefaction analysis, and outputs the plots in ggplot2
  format for further facetting and customisation. After clustering, CAGEr performs
  analyses of promoter width and detects differential usage of TSSs (promoter shifting)
  between samples. CAGEr also exports its data as genome browser tracks, and as R
  objects for downsteam expression analysis by other Bioconductor packages such as
  DESeq2, CAGEfightR, or seqArchR.
authors:
- family-names: Haberle
  given-names: Vanja
  email: vanja.haberle@gmail.com
- family-names: Plessy
  given-names: Charles
  email: charles.plessy@oist.jp
preferred-citation:
  type: article
  title: 'CAGEr: precise TSS data retrieval and high-resolution promoterome mining
    for integrative analyses'
  authors:
  - family-names: Haberle
    given-names: Vanja
    email: vanja.haberle@gmail.com
  - family-names: Forrest
    given-names: Alistair R R
  - family-names: Hayashizaki
    given-names: Yoshihide
  - family-names: Carninci
    given-names: Piero
  - family-names: Lenhard
    given-names: Boris
  year: '2015'
  journal: Nucleic Acids Research
  volume: '43'
  issue: '8'
  doi: 10.1093/nar/gkv054
  url: http://nar.oxfordjournals.org/content/43/8/e51
  start: e51
repository: https://bioc.r-universe.dev
date-released: '2024-05-24'
contact:
- family-names: Plessy
  given-names: Charles
  email: charles.plessy@oist.jp