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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 "sctransform" in publications use:'
type: software
license: GPL-3.0-only
title: 'sctransform: Variance Stabilizing Transformations for Single Cell UMI Data'
version: 0.4.1
doi: 10.1186/s13059-019-1874-1
identifiers:
- type: doi
  value: 10.32614/CRAN.package.sctransform
abstract: A normalization method for single-cell UMI count data using a variance stabilizing
  transformation. The transformation is based on a negative binomial regression model
  with regularized parameters. As part of the same regression framework, this package
  also provides functions for batch correction, and data correction. See Hafemeister
  and Satija (2019) <https://doi.org/10.1186/s13059-019-1874-1>, and Choudhary and
  Satija (2022) <https://doi.org/10.1186/s13059-021-02584-9> for more details.
authors:
- family-names: Hafemeister
  given-names: Christoph
  email: christoph.hafemeister@nyu.edu
  orcid: https://orcid.org/0000-0001-6365-8254
- family-names: Choudhary
  given-names: Saket
  email: schoudhary@nygenome.org
  orcid: https://orcid.org/0000-0001-5202-7633
preferred-citation:
  type: article
  title: Normalization and variance stabilization of single-cell RNA-seq data using
    regularized negative binomial regression
  authors:
  - family-names: Hafemeister
    given-names: Christoph
    email: christoph.hafemeister@nyu.edu
    orcid: https://orcid.org/0000-0001-6365-8254
  - family-names: Satija
    given-names: Rahul
    email: rsatija@nygenome.org
    orcid: https://orcid.org/000 -0001-9448-8833
  journal: Genome Biology
  year: '2019'
  volume: '20'
  doi: 10.1186/s13059-019-1874-1
  url: https://doi.org/10.1186/s13059-019-1874-1
  start: '296'
repository: https://CRAN.R-project.org/package=sctransform
repository-code: https://github.com/satijalab/sctransform
url: https://github.com/satijalab/sctransform
date-released: '2023-10-18'
contact:
- family-names: Choudhary
  given-names: Saket
  email: schoudhary@nygenome.org
  orcid: https://orcid.org/0000-0001-5202-7633
references:
- type: article
  title: Comparison and evaluation of statistical error models for scRNA-seq
  authors:
  - family-names: Choudhary
    given-names: Saket
    email: schoudhary@nygenome.org
    orcid: https://orcid.org/0000-0001-5202-7633
  - family-names: Satija
    given-names: Rahul
    email: rsatija@nygenome.org
    orcid: https://orcid.org/0000-0001-9448-8833
  journal: Genome Biology
  year: '2022'
  volume: '23'
  doi: 10.1186/s13059-021-02584-9
  url: https://doi.org/10.1186/s13059-021-02584-9
  start: '20'