# --------------------------------------------
# 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 "QuasR" in publications use:'
type: software
license: GPL-2.0-only
title: 'QuasR: Quantify and Annotate Short Reads in R'
version: 1.45.1
doi: 10.1093/bioinformatics/btu781
abstract: This package provides a framework for the quantification and analysis of
  Short Reads. It covers a complete workflow starting from raw sequence reads, over
  creation of alignments and quality control plots, to the quantification of genomic
  regions of interest. Read alignments are either generated through Rbowtie (data
  from DNA/ChIP/ATAC/Bis-seq experiments) or Rhisat2 (data from RNA-seq experiments
  that require spliced alignments), or can be provided in the form of bam files.
authors:
- family-names: Lerch
  given-names: Anita
- family-names: SMITH
  given-names: Adam Alexander Thil
  email: alex.smith@fmi.ch
  orcid: https://orcid.org/0000-0003-4593-3042
- family-names: Soneson
  given-names: Charlotte
  email: charlottesoneson@gmail.com
  orcid: https://orcid.org/0000-0003-3833-2169
- family-names: Gaidatzis
  given-names: Dimos
- family-names: Stadler
  given-names: Michael
  email: michael.stadler@fmi.ch
  orcid: https://orcid.org/0000-0002-2269-4934
preferred-citation:
  type: article
  title: 'QuasR: Quantification and annotation of short reads in R'
  authors:
  - family-names: Gaidatzis
    given-names: Dimos
  - family-names: Lerch
    given-names: Anita
  - family-names: Hahne
    given-names: Florian
  - family-names: Stadler
    given-names: Michael B
  journal: Bioinformatics
  volume: '31'
  issue: '7'
  year: '2015'
  notes: PMID:25417205
  doi: 10.1093/bioinformatics/btu781
  start: '1130'
  end: '1132'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/fmicompbio/QuasR
url: https://bioconductor.org/packages/QuasR
date-released: '2024-03-14'
contact:
- family-names: Stadler
  given-names: Michael
  email: michael.stadler@fmi.ch
  orcid: https://orcid.org/0000-0002-2269-4934
references:
- type: article
  title: Ultrafast and memory-efficient alignment of short DNA sequences to the human
    genome
  authors:
  - family-names: Langmead
    given-names: Ben
  - family-names: Trapnell
    given-names: Cole
  - family-names: Pop
    given-names: Mihai
  - family-names: Salzberg
    given-names: Steven L
  journal: Genome Biology
  volume: '10'
  issue: '3'
  year: '2009'
  notes: PMID:19261174
  doi: 10.1186/gb-2009-10-3-r25
  start: R25
- type: article
  title: Detection of splice junctions from paired-end RNA-seq data by SpliceMap
  authors:
  - family-names: Au
    given-names: Kin Fai
  - family-names: Jiang
    given-names: Hui
  - family-names: Lin
    given-names: Lan
  - family-names: Xing
    given-names: Yi
  - family-names: Wong
    given-names: Wing Hung
  journal: Nucleic Acids Research
  volume: '38'
  issue: '14'
  year: '2010'
  notes: PMID:20371516
  doi: 10.1093/nar/gkq211
  start: '4570'
  end: '4578'
- type: article
  title: 'HISAT: a fast spliced aligner with low memory requirements'
  authors:
  - family-names: Kim
    given-names: Daehwan
  - family-names: Langmead
    given-names: Ben
  - family-names: Salzberg
    given-names: Steven L
  journal: Nature Methods
  volume: '12'
  year: '2015'
  notes: PMID:25751142
  doi: 10.1038/nmeth.3317
  start: '357'
  end: '360'