Package: DCATS 1.5.0

Xinyi Lin

DCATS: Differential Composition Analysis Transformed by a Similarity matrix

Methods to detect the differential composition abundances between conditions in singel-cell RNA-seq experiments, with or without replicates. It aims to correct bias introduced by missclaisification and enable controlling of confounding covariates. To avoid the influence of proportion change from big cell types, DCATS can use either total cell number or specific reference group as normalization term.

Authors:Xinyi Lin [aut, cre], Chuen Chau [aut], Yuanhua Huang [aut], Joshua W.K. Ho [aut]

DCATS_1.5.0.tar.gz
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DCATS_1.5.0.tgz(r-4.4-any)DCATS_1.5.0.tgz(r-4.3-any)
DCATS_1.5.0.tar.gz(r-4.5-noble)DCATS_1.5.0.tar.gz(r-4.4-noble)
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DCATS.pdf |DCATS.html✨
DCATS/json (API)
NEWS

# Install 'DCATS' in R:
install.packages('DCATS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Datasets:
  • Haber2017 - Count matrices of intestinal epithelial scRNA-seq data from three conditions
  • Kang2017 - Count matrices of 8 pooled lupus patient samples within two conditions
  • Ren2021 - Count matrix and metadata of a large COVID-19 scRNA-seq data cohort.
  • simulation - Simulated dataset with two conditions

On BioConductor:DCATS-1.5.0(bioc 3.21)DCATS-1.4.0(bioc 3.20)

This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.

singlecellnormalization

4.53 score 34 scripts 152 downloads 8 exports 17 dependencies

Last updated 2 months agofrom:61682fd083. Checks:OK: 1 NOTE: 6. Indexed: yes.

TargetResultDate
Doc / VignettesOKNov 29 2024
R-4.5-winNOTENov 29 2024
R-4.5-linuxNOTENov 29 2024
R-4.4-winNOTENov 29 2024
R-4.4-macNOTENov 29 2024
R-4.3-winNOTENov 29 2024
R-4.3-macNOTENov 29 2024

Exports:create_simMatdcats_GLMdetect_referencegetPhiknn_simMatmultinom_EMsimulator_basesvm_simMat

Dependencies:aodclasscodaDEoptimRe1071latticeMASSMatrixMatrixModelsmatrixStatsmcmcMCMCpackproxyquantregrobustbaseSparseMsurvival

Differential Composition Analysis with DCATS

Xinyi LIN

Rendered fromIntro_to_DCATS.Rmdusingknitr::rmarkdownon Nov 29 2024.

Last update: 2023-04-21
Started: 2022-11-16