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# CITATION file created with {cffr} R package
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cff-version: 1.2.0
message: 'To cite package "ppcseq" in publications use:'
type: software
license: GPL-3.0-only
title: 'ppcseq: Probabilistic Outlier Identification for RNA Sequencing Generalized
  Linear Models'
version: 1.13.0
identifiers:
- type: doi
  value: 10.32614/CRAN.package.ppcseq
abstract: Relative transcript abundance has proven to be a valuable tool for understanding
  the function of genes in biological systems. For the differential analysis of transcript
  abundance using RNA sequencing data, the negative binomial model is by far the most
  frequently adopted. However, common methods that are based on a negative binomial
  model are not robust to extreme outliers, which we found to be abundant in public
  datasets. So far, no rigorous and probabilistic methods for detection of outliers
  have been developed for RNA sequencing data, leaving the identification mostly to
  visual inspection. Recent advances in Bayesian computation allow large-scale comparison
  of observed data against its theoretical distribution given in a statistical model.
  Here we propose ppcseq, a key quality-control tool for identifying transcripts that
  include outlier data points in differential expression analysis, which do not follow
  a negative binomial distribution. Applying ppcseq to analyse several publicly available
  datasets using popular tools, we show that from 3 to 10 percent of differentially
  abundant transcripts across algorithms and datasets had statistics inflated by the
  presence of outliers.
authors:
- family-names: Mangiola
  given-names: Stefano
  email: mangiolastefano@gmail.com
  orcid: https://orcid.org/0000-0001-7474-836X
preferred-citation:
  type: article
  title: Probabilistic outlier identification for RNA sequencing generalized linear
    models
  authors:
  - family-names: Mangiola
    given-names: Stefano
    email: mangiolastefano@gmail.com
    orcid: https://orcid.org/0000-0001-7474-836X
  - family-names: Thomas
    given-names: Evan
  - family-names: Modrak
    given-names: Martin
  - family-names: Vehtari
    given-names: Aki
  - family-names: Papenfuss
    given-names: Anthony
  journal: NAR Genomics and Bioinformatics
  year: '2021'
  volume: '3'
  issue: '1'
  notes: R package version 1.13.0
  url: https://doi.org/10.1093/nargab/lqab005
  start: lqab005
repository: https://bioc.r-universe.dev
repository-code: https://github.com/stemangiola/ppcseq
commit: 9168270474c99e73ca9f8b0bb71924a5fa0cbf2d
url: https://github.com/stemangiola/ppcseq
contact:
- family-names: Mangiola
  given-names: Stefano
  email: mangiolastefano@gmail.com
  orcid: https://orcid.org/0000-0001-7474-836X