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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 "fastTopics" in publications use:'
type: software
license: BSD-2-Clause
title: 'fastTopics: Fast Algorithms for Fitting Topic Models and Non-Negative Matrix
  Factorizations to Count Data'
version: 0.6-192
identifiers:
- type: doi
  value: 10.32614/CRAN.package.fastTopics
abstract: Implements fast, scalable optimization algorithms for fitting topic models
  ("grade of membership" models) and non-negative matrix factorizations to count data.
  The methods exploit the special relationship between the multinomial topic model
  (also, "probabilistic latent semantic indexing") and Poisson non-negative matrix
  factorization. The package provides tools to compare, annotate and visualize model
  fits, including functions to efficiently create "structure plots" and identify key
  features in topics. The 'fastTopics' package is a successor to the 'CountClust'
  package. For more information, see <https://doi.org/10.48550/arXiv.2105.13440> and
  <https://doi.org/10.1186/s13059-023-03067-9>. Please also see the GitHub repository
  for additional vignettes not included in the package on CRAN.
authors:
- family-names: Carbonetto
  given-names: Peter
  email: peter.carbonetto@gmail.com
- family-names: Luo
  given-names: Kevin
- family-names: Dey
  given-names: Kushal
- family-names: Stephens
  given-names: Matthew
preferred-citation:
  type: article
  title: Visualizing the structure of RNA-seq expression data using grade of membership
    models
  authors:
  - name: Kushal K. Dey
  - name: Chiaowen Joyce Hsiao
  - name: Matthew Stephens
  journal: PLoS Genetics
  volume: '13'
  issue: '3'
  year: '2017'
  url: https://doi.org/10.1371/journal.pgen.1006599
  start: e1006599
repository: https://stephenslab.r-universe.dev
repository-code: https://github.com/stephenslab/fastTopics
commit: 0738d0a5d71e6795e85805c58aa342c3fb9e6bd9
url: https://stephenslab.github.io/fastTopics/
date-released: '2024-07-08'
contact:
- family-names: Carbonetto
  given-names: Peter
  email: peter.carbonetto@gmail.com
references:
- type: article
  title: Non-negative matrix factorization algorithms greatly improve topic model
    fits
  authors:
  - name: Peter Carbonetto
  - name: Abhishek Sarkar
  - name: Zihao Wang
  - name: Matthew Stephens
  journal: arXiv
  volume: '2105.13440'
  year: '2021'
  url: https://arxiv.org/abs/2105.13440
- type: article
  title: Interpreting structure in sequence count data with differential expression
    analysis allowing for grades of membership
  authors:
  - name: Peter Carbonetto
  - name: Kaixuan Luo
  - name: Abhishek Sarkar
  - name: Anthony Hung
  - name: Karl Tayeb
  - name: Sebastian Pott
  - name: Matthew Stephens
  journal: Genome Biology
  doi: 10.1186/s13059-023-03067-9
  volume: '24'
  year: '2023'
  start: '236'