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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 "TOAST" in publications use:'
type: software
license: GPL-2.0-only
title: 'TOAST: Tools for the analysis of heterogeneous tissues'
version: 1.19.0
abstract: This package is devoted to analyzing high-throughput data (e.g. gene expression
  microarray, DNA methylation microarray, RNA-seq) from complex tissues. Current functionalities
  include 1. detect cell-type specific or cross-cell type differential signals 2.
  tree-based differential analysis 3. improve variable selection in reference-free
  deconvolution 4. partial reference-free deconvolution with prior knowledge.
authors:
- family-names: Li
  given-names: Ziyi
  email: zli16@mdanderson.org
- family-names: Zhang
  given-names: Weiwei
- family-names: Chen
  given-names: Luxiao
- family-names: Wu
  given-names: Hao
preferred-citation:
  type: article
  title: Dissecting differential signals in high-throughput data from complex tissues
  authors:
  - family-names: Li
    given-names: Ziyi
    email: zli16@mdanderson.org
  - family-names: Wu
    given-names: Zhijin
  - family-names: Jin
    given-names: Peng
  - family-names: Wu
    given-names: Hao
  year: '2019'
  journal: Bioinformatics
  volume: '35'
  issue: '20'
  start: '7803'
repository: https://bioc.r-universe.dev
repository-code: https://github.com/ziyili20/TOAST
url: https://github.com/ziyili20/TOAST
date-released: '2022-08-14'
contact:
- family-names: Li
  given-names: Ziyi
  email: zli16@mdanderson.org
references:
- type: article
  title: 'TOAST: improving reference-free cell composition estimation by cross-cell
    type differential analysis'
  authors:
  - family-names: Li
    given-names: Ziyi
  - family-names: Wu
    given-names: Hao
  year: '2019'
  journal: Genome Biology
  volume: '20'
  issue: '1'
  start: '18'
- type: article
  title: Robust partial reference-free cell composition estimation from tissue expression
  authors:
  - family-names: Li
    given-names: Ziyi
  - family-names: Guo
    given-names: Zhenxing
  - family-names: Cheng
    given-names: Ying
  - family-names: Jin
    given-names: Peng
  - family-names: Wu
    given-names: Hao
  year: '2020'
  journal: Bioinformatics
  volume: '36'
  issue: '11'
  start: '6869'
- type: article
  title: 'Complete deconvolution of DNA methylation signals from complex tissues:
    a geometric approach'
  authors:
  - family-names: Zhang
    given-names: Weiwei
  - family-names: Wu
    given-names: Hao
  - family-names: Li
    given-names: Ziyi
  year: '2020'
  journal: Bioinformatics
  volume: '37'
  issue: '8'
  start: '-7'