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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 "BatchQC" in publications use:'
type: software
license: MIT
title: 'BatchQC: Batch Effects Quality Control Software'
version: 2.1.2
doi: 10.1093/bioinformatics/btw538
abstract: 'Sequencing and microarray samples often are collected or processed in multiple
  batches or at different times. This often produces technical biases that can lead
  to incorrect results in the downstream analysis. BatchQC is a software tool that
  streamlines batch preprocessing and evaluation by providing interactive diagnostics,
  visualizations, and statistical analyses to explore the extent to which batch variation
  impacts the data. BatchQC diagnostics help determine whether batch adjustment needs
  to be done, and how correction should be applied before proceeding with a downstream
  analysis. Moreover, BatchQC interactively applies multiple common batch effect approaches
  to the data and the user can quickly see the benefits of each method. BatchQC is
  developed as a Shiny App. The output is organized into multiple tabs and each tab
  features an important part of the batch effect analysis and visualization of the
  data. The BatchQC interface has the following analysis groups: Summary, Differential
  Expression, Median Correlations, Heatmaps, Circular Dendrogram, PCA Analysis, Shape,
  ComBat and SVA.'
authors:
- family-names: McClintock
  given-names: Jessica
  email: jessica.mcclintock@rutgers.edu
  orcid: https://orcid.org/0000-0002-0542-9872
- family-names: Johnson
  given-names: W. Evan
  email: wj183@njms.rutgers.edu
  orcid: https://orcid.org/0000-0002-6247-6595
- family-names: Manimaran
  given-names: Solaiappan
  email: manimaran_1975@hotmail.com
- family-names: Holmes
  given-names: Evan
  email: evanjh19@gmail.com
preferred-citation:
  type: article
  title: 'BatchQC: interactive software for evaluating sample and batch effects in
    genomic data'
  authors:
  - family-names: Manimaran
    given-names: Solaiappan
    email: manimaran_1975@hotmail.com
  - family-names: Selby
    given-names: Heather Marie
  - family-names: Okrah
    given-names: Kwame
  - family-names: Ruberman
    given-names: Claire
  - family-names: Leek
    given-names: Jeffrey T.
  - family-names: Quackenbush
    given-names: John
  - family-names: Haibe-Kains
    given-names: Benjamin
  - family-names: Bravo
    given-names: Hector Corrada
  - family-names: Johnson
    given-names: W. Evan
    email: wj183@njms.rutgers.edu
    orcid: https://orcid.org/0000-0002-6247-6595
  year: '2016'
  journal: Bioinformatics
  doi: 10.1093/bioinformatics/btw538
  url: http://bioinformatics.oxfordjournals.org/content/early/2016/08/30/bioinformatics.btw538
repository: https://bioc.r-universe.dev
repository-code: https://github.com/wejlab/BatchQC
url: https://github.com/wejlab/BatchQC
date-released: '2024-05-21'
contact:
- family-names: McClintock
  given-names: Jessica
  email: jessica.mcclintock@rutgers.edu
  orcid: https://orcid.org/0000-0002-0542-9872