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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 "geneXtendeR" in publications use:'
type: software
license: GPL-3.0-or-later
title: 'geneXtendeR: Optimized Functional Annotation Of ChIP-seq Data'
version: 1.31.0
abstract: geneXtendeR optimizes the functional annotation of ChIP-seq peaks by exploring
  relative differences in annotating ChIP-seq peak sets to variable-length gene bodies.
  In contrast to prior techniques, geneXtendeR considers peak annotations beyond just
  the closest gene, allowing users to see peak summary statistics for the first-closest
  gene, second-closest gene, ..., n-closest gene whilst ranking the output according
  to biologically relevant events and iteratively comparing the fidelity of peak-to-gene
  overlap across a user-defined range of upstream and downstream extensions on the
  original boundaries of each gene's coordinates. Since different ChIP-seq peak callers
  produce different differentially enriched peaks with a large variance in peak length
  distribution and total peak count, annotating peak lists with their nearest genes
  can often be a noisy process. As such, the goal of geneXtendeR is to robustly link
  differentially enriched peaks with their respective genes, thereby aiding experimental
  follow-up and validation in designing primers for a set of prospective gene candidates
  during qPCR.
authors:
- family-names: Khomtchouk
  given-names: Bohdan
  email: khomtchoukmed@gmail.com
- family-names: Koehler
  given-names: William
  email: williamk03hler@gmail.com
preferred-citation:
  type: article
  title: Optimized functional annotation of ChIP-seq data
  authors:
  - family-names: Khomtchouk
    given-names: Bohdan
    email: khomtchoukmed@gmail.com
  - family-names: Koehler
    given-names: William
    email: williamk03hler@gmail.com
  - family-names: Van Booven
    given-names: Derek
  - family-names: Wahlestedt
    given-names: Claes
  journal: bioRxiv
  year: '2018'
  issue: R package version 1.8.0
repository: https://bioc.r-universe.dev
repository-code: https://github.com/Bohdan-Khomtchouk/geneXtendeR
url: https://github.com/Bohdan-Khomtchouk/geneXtendeR
contact:
- family-names: Khomtchouk
  given-names: Bohdan
  email: khomtchoukmed@gmail.com