# ------------------------------------------------
# CITATION.cff file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# ------------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "TSSr" in publications use:'
type: software
license: MIT
title: 'TSSr: TSS sequencing data analysis'
version: 0.99.21
doi: 10.1093/nargab/lqab108
abstract: TSSr package provides a comprehensive workflow on TSS data starts from identification
  of accurate TSS locations, clustering TSSs within small genomic regions corresponding
  to core promoters, and transcriptional activity quantifications, as well as specialized
  downstream analyses including core promoter shape, cluster annotation, gene differential
  expression, core promoter shift. TSSr can take multiple formats of files as input,
  such as Binary Sequence Alignment Map (BAM) files (single-ended or paired-ended),
  Browser Extension Data (bed) files, BigWig files, ctss files or tss tables. TSSr
  also generates various types of TSS or core promoter track files which can be visualized
  in the UCSC Genome Browser or Integrative Genomics Viewer (IGV). TSSr also exports
  downstream analyses result tables and plots. Multiple cores are supported on Linux
  or Mac platforms.
authors:
- family-names: Lu
  given-names: Zhaolian
  email: luzhaolian@gmail.com
  orcid: https://orcid.org/0000-0001-5002-7007
- family-names: Berry
  given-names: Keenan
  email: keenan.berry@slu.edu
- family-names: Hu
  given-names: Zhenbin
  email: zhenbin.hu@slu.edu
- family-names: Zhan
  given-names: Yu
  email: yu.zhan@slu.edu
- family-names: Ahn
  given-names: Tae-Hyuk (Ted)
  email: ted.ahn@slu.edu
- family-names: Lin
  given-names: Zhenguo
  email: zhenguo.lin@slu.edu
  orcid: https://orcid.org/0000-0002-8400-9138
preferred-citation:
  type: article
  title: 'TSSr: an R package for comprehensive analyses of TSS sequencing data'
  authors:
  - family-names: Lu
    given-names: Zhaolian
    email: luzhaolian@gmail.com
    orcid: https://orcid.org/0000-0001-5002-7007
  - family-names: Berry
    given-names: Keenan
    email: keenan.berry@slu.edu
  - family-names: Hu
    given-names: Zhenbin
    email: zhenbin.hu@slu.edu
  - family-names: Zhan
    given-names: Yu
    email: yu.zhan@slu.edu
  - family-names: Ahn
    given-names: Tae-Hyuk
  - family-names: Lin
    given-names: Zhenguo
    email: zhenguo.lin@slu.edu
    orcid: https://orcid.org/0000-0002-8400-9138
  journal: NAR Genomics and Bioinformatics
  year: '2021'
  volume: '3'
  issue: '4'
  doi: 10.1093/nargab/lqab108
  start: lqab108
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Linlab-slu/TSSr
commit: bba29ddb31aa3bcc5c8e1a4276224de759b5b7ea
url: https://github.com/Linlab-slu/TSSr
date-released: '2026-08-21'
contact:
- family-names: Lin
  given-names: Zhenguo
  email: zhenguo.lin@slu.edu
  orcid: https://orcid.org/0000-0002-8400-9138