Package: diffcyt 1.25.0

Lukas M. Weber

diffcyt: Differential discovery in high-dimensional cytometry via high-resolution clustering

Statistical methods for differential discovery analyses in high-dimensional cytometry data (including flow cytometry, mass cytometry or CyTOF, and oligonucleotide-tagged cytometry), based on a combination of high-resolution clustering and empirical Bayes moderated tests adapted from transcriptomics.

Authors:Lukas M. Weber [aut, cre]

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NEWS

# Install 'diffcyt' in R:

install.packages('diffcyt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/lmweber/diffcyt/issues

On BioConductor:diffcyt-1.25.0(bioc 3.20)diffcyt-1.24.0(bioc 3.19)

bioconductor-package

19 exports 1.80 score 144 dependencies 4 dependents 18 mentions

Last updated 2 months agofrom:c7912075f9

Exports:calcCounts calcMedians calcMediansByClusterMarker calcMediansBySampleMarker createContrast createDesignMatrix createFormula diffcyt generateClusters plotHeatmap prepareData testDA_edgeR testDA_GLMM testDA_voom testDS_limma testDS_LMM topClusters topTable transformData

Dependencies:abind ALL askpass backports BH Biobase BiocGenerics boot brio broom callr car carData circlize cli clue cluster codetools colorRamps colorspace ComplexHeatmap ConsensusClusterPlus corrplot cowplot cpp11 crayon curl cytolib DelayedArray desc diffobj digest doParallel dplyr edgeR evaluate fansi farver flowCore FlowSOM foreach fs generics GenomeInfoDb GenomeInfoDbData GenomicRanges GetoptLong ggforce ggnewscale ggplot2 ggpubr ggrepel ggsci ggsignif GlobalOptions glue gridExtra gtable httr igraph IRanges isoband iterators jsonlite labeling lattice lifecycle limma lme4 locfit magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats mgcv mime minqa multcomp munsell mvtnorm nlme nloptr nnet numDeriv openssl pbkrtest pillar pkgbuild pkgconfig pkgload plyr png polyclip polynom praise processx ps purrr quantreg R6 RColorBrewer Rcpp RcppEigen rematch2 reshape2 Rhdf5lib rjson rlang rprojroot RProtoBufLib rstatix Rtsne S4Arrays S4Vectors sandwich scales shape SparseArray SparseM statmod stringi stringr SummarizedExperiment survival sys systemfonts testthat TH.data tibble tidyr tidyselect tweenr UCSC.utils utf8 vctrs viridisLite waldo withr XML XVector zlibbioc zoo

diffcyt workflow

Lukas M. Weber, Malgorzata Nowicka, Charlotte Soneson, Mark. D. Robinson

Rendered fromdiffcyt_workflow.Rmdusingknitr::rmarkdownon Jun 12 2024.

Last update: 2019-03-29
Started: 2018-03-28

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
Calculate cluster cell counts	calcCounts
Calculate cluster medians	calcMedians
Calculate medians (by cluster and marker)	calcMediansByClusterMarker
Calculate medians (by sample and marker)	calcMediansBySampleMarker
Create contrast matrix	createContrast
Create design matrix	createDesignMatrix
Create model formula and corresponding data frame of variables	createFormula
Run 'diffcyt' pipeline	diffcyt-package diffcyt
Generate clusters	generateClusters
Plot heatmap	plotHeatmap
Prepare data	prepareData
Test for differential abundance: method 'diffcyt-DA-edgeR'	testDA_edgeR
Test for differential abundance: method 'diffcyt-DA-GLMM'	testDA_GLMM
Test for differential abundance: method 'diffcyt-DA-voom'	testDA_voom
Test for differential states: method 'diffcyt-DS-limma'	testDS_limma
Test for differential states: method 'diffcyt-DS-LMM'	testDS_LMM
Alias for 'topTable' (deprecated)	topClusters
Show table of results for top clusters or cluster-marker combinations	topTable
Transform data	transformData