Package: TOAST 1.19.0
TOAST: Tools for the analysis of heterogeneous tissues
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:
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NEWS
# Install 'TOAST' in R: |
install.packages('TOAST', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ziyili20/toast/issues
- CBS_PBMC_array - An example dataset for partial reference-free cell composition estimation from tissue gene expression
- RA_100samples - An example dataset for cellular proportion estimation and multiple factor design
- beta_emp - Simulated methylation 450K array data with related
On BioConductor:TOAST-1.19.0(bioc 3.20)TOAST-1.18.0(bioc 3.19)
Last updated 2 months agofrom:81d1be10cd
Exports:assignCellTypecedarChooseMarkercsDeconvcsTestDEVarSelectfindRefinxfitModelGetPriormakeDesignMDeconvmyprojectMixmyRefFreeCellMixmyRefFreeCellMixInitializeplotCorrTsisal
Dependencies:abindaskpassbackportsBiobaseBiocGenericsbitbit64broombroom.helpersclassclicliprcodetoolscolorspacecorpcorcpp11crayoncurlDelayedArraydoParalleldplyre1071EpiDISHfansifarverforcatsforeachgenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGGallyggplot2ggstatsgluegtablehavenhmshttrIRangesisobanditeratorsjsonlitelabelinglabelledlatticelifecyclelimmalocfdrmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmimemunsellnlmennlsopensslpatchworkpillarpkgconfigplyrprettyunitsprogressproxypurrrquadprogR6RColorBrewerRcppreadrrlangS4ArraysS4VectorsscalesSparseArraystatmodstringistringrSummarizedExperimentsystibbletidyrtidyselecttzdbUCSC.utilsutf8vctrsviridisLitevroomwithrXVectorzlibbioc