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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 "rmspc" in publications use:'
type: software
license: GPL-3.0-only
title: 'rmspc: Multiple Sample Peak Calling'
version: 1.11.0
doi: 10.1093/bioinformatics/btv293
abstract: The rmspc package runs MSPC (Multiple Sample Peak Calling) software using
  R. The analysis of ChIP-seq samples outputs a number of enriched regions (commonly
  known as "peaks"), each indicating a protein-DNA interaction or a specific chromatin
  modification. When replicate samples are analyzed, overlapping peaks are expected.
  This repeated evidence can therefore be used to locally lower the minimum significance
  required to accept a peak. MSPC uses combined evidence from replicated experiments
  to evaluate peak calling output, rescuing peaks, and reduce false positives. It
  takes any number of replicates as input and improves sensitivity and specificity
  of peak calling on each, and identifies consensus regions between the input samples.
authors:
- family-names: Jalili
  given-names: Vahid
  email: jalili.vahid@gmail.com
- family-names: Cremona
  given-names: Marzia Angela
  email: marzia.cremona@fsa.ulaval.ca
- family-names: Palluzzi
  given-names: Fernando
  email: fernando.palluzzi@gmail.com
- family-names: Bahda
  given-names: Meriem
  email: meriembahda@gmail.com
preferred-citation:
  type: article
  title: Using combined evidence from replicates to evaluate ChIP-seq peaks.
  authors:
  - family-names: Jalili
    given-names: Vahid
    email: jalili.vahid@gmail.com
  - family-names: Matteucci
    given-names: Matteo
  - family-names: Masseroli
    given-names: Marco
  - family-names: Morelli
    given-names: Marco J
  year: '2015'
  journal: Bioinformatics
  volume: '31'
  issue: '17'
  doi: 10.1093/bioinformatics/btv293
  url: https://academic.oup.com/bioinformatics/article/31/17/2761/183989
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Genometric/MSPC
url: https://genometric.github.io/MSPC/
contact:
- family-names: Bahda
  given-names: Meriem
  email: meriembahda@gmail.com