# --------------------------------------------
# CITATION file created with {cffr} R package
# See also: https://docs.ropensci.org/cffr/
# --------------------------------------------
 
cff-version: 1.2.0
message: 'To cite package "seqArchR" in publications use:'
type: software
license: GPL-3.0-only
title: 'seqArchR: Identify Different Architectures of Sequence Elements'
version: 1.9.0
doi: 10.18129/B9.bioc.seqArchR
abstract: seqArchR enables unsupervised discovery of _de novo_ clusters with characteristic
  sequence architectures characterized by position-specific motifs or composition
  of stretches of nucleotides, e.g., CG-richness. seqArchR does _not_ require any
  specifications w.r.t. the number of clusters, the length of any individual motifs,
  or the distance between motifs if and when they occur in pairs/groups; it directly
  detects them from the data. seqArchR uses non-negative matrix factorization (NMF)
  as its backbone, and employs a chunking-based iterative procedure that enables processing
  of large sequence collections efficiently. Wrapper functions are provided for visualizing
  cluster architectures as sequence logos.
authors:
- family-names: Nikumbh
  given-names: Sarvesh
  email: sarvesh.nikumbh@gmail.com
  orcid: https://orcid.org/0000-0003-3163-4447
preferred-citation:
  type: manual
  title: 'seqArchR: an R/Bioconductor package for identifying promoter sequence architectures'
  authors:
  - family-names: Nikumbh
    given-names: Sarvesh
    email: sarvesh.nikumbh@gmail.com
    orcid: https://orcid.org/0000-0003-3163-4447
  year: '2024'
  url: http://www.bioconductor.org/packages/seqArchR
  doi: 10.18129/B9.bioc.seqArchR
repository: https://bioc.r-universe.dev
repository-code: https://github.com/snikumbh/seqArchR
url: https://snikumbh.github.io/seqArchR/
contact:
- family-names: Nikumbh
  given-names: Sarvesh
  email: sarvesh.nikumbh@gmail.com
  orcid: https://orcid.org/0000-0003-3163-4447