Package: muscat 1.21.0
Helena L. Crowell
muscat: Multi-sample multi-group scRNA-seq data analysis tools
`muscat` provides various methods and visualization tools for DS analysis in multi-sample, multi-group, multi-(cell-)subpopulation scRNA-seq data, including cell-level mixed models and methods based on aggregated “pseudobulk” data, as well as a flexible simulation platform that mimics both single and multi-sample scRNA-seq data.
Authors:
muscat_1.21.0.tar.gz
muscat_1.21.0.zip(r-4.5)muscat_1.21.0.zip(r-4.4)muscat_1.19.0.zip(r-4.3)
muscat_1.21.0.tgz(r-4.4-any)muscat_1.19.0.tgz(r-4.3-any)
muscat_1.21.0.tar.gz(r-4.5-noble)muscat_1.21.0.tar.gz(r-4.4-noble)
muscat_1.21.0.tgz(r-4.4-emscripten)muscat_1.19.0.tgz(r-4.3-emscripten)
muscat.pdf |muscat.html✨
muscat/json (API)
NEWS
| # Install 'muscat' in R: |
| install.packages('muscat', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/helenalc/muscat/issues
- example_sce - Example datasets
On BioConductor:muscat-1.21.0(bioc 3.21)muscat-1.20.0(bioc 3.20)
immunooncologydifferentialexpressionsequencingsinglecellsoftwarestatisticalmethodvisualization
Last updated 2 months agofrom:0bf2615408. Checks:OK: 1 NOTE: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | OK | Nov 29 2024 |
| R-4.5-win | NOTE | Nov 29 2024 |
| R-4.5-linux | NOTE | Nov 29 2024 |
| R-4.4-win | NOTE | Nov 29 2024 |
| R-4.4-mac | NOTE | Nov 29 2024 |
| R-4.3-win | NOTE | Sep 28 2024 |
| R-4.3-mac | NOTE | Sep 28 2024 |
Exports:aggregateDatacalcExprFreqsmmDSpbDDpbDSpbFlattenpbHeatmappbMDSprepSCEprepSimresDSsimDatastagewise_DS_DD
Dependencies:abindaodaskpassassortheadbackportsbeachmatbeeswarmBHBiobaseBiocGenericsBiocNeighborsBiocParallelBiocSingularbitopsblmebootbroomCairocaToolscirclizecliclueclustercodetoolscolorspaceComplexHeatmapcorpcorcowplotcpp11crayoncurldata.tableDelayedArrayDerivDESeq2digestdoBydoParalleldplyrdqrngedgeREnvStatsfANCOVAfansifarverFNNforeachformatRfutile.loggerfutile.optionsfuturefuture.applygenericsGenomeInfoDbGenomeInfoDbDataGenomicRangesGetoptLongggbeeswarmggplot2ggrastrggrepelglmmTMBGlobalOptionsglobalsgluegplotsgridExtragtablegtoolshmshttrIRangesirlbaisobanditeratorsjsonliteKernSmoothlabelinglambda.rlatticelifecyclelimmalistenvlme4lmerTestlocfitmagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmicrobenchmarkmimeminqamodelrmunsellmvtnormnlmenloptrnortestnumDerivopensslparallellypbkrtestpheatmappillarpkgconfigplyrpngprettyunitsprogresspurrrR6raggrbibutilsRColorBrewerRcppRcppAnnoyRcppArmadilloRcppEigenRcppMLRcppProgressRdpackreformulasremaCorreshape2RhpcBLASctlrjsonrlangRSpectrarsvdRtsneS4ArraysS4VectorsScaledMatrixscalesscatersctransformscuttleshapeSingleCellExperimentsitmosnowSparseArraystatmodstringistringrSummarizedExperimentsyssystemfontstextshapingtibbletidyrtidyselectTMBUCSC.utilsutf8uwotvariancePartitionvctrsviporviridisviridisLitewithrXVectorzlibbioc
Differential state analysis with muscat
Rendered fromanalysis.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-10-07
Started: 2020-02-04
Simulating complex design scRNA-seq data with muscat
Rendered fromsimulation.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-10-07
Started: 2020-02-04
Differential detection analysis
Rendered fromdetection.Rmdusingknitr::rmarkdownon Nov 29 2024.Last update: 2024-10-07
Started: 2024-10-07
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Aggregation of single-cell to pseudobulk data | aggregateData |
| calcExprFreqs | calcExprFreqs |
| Example datasets | data example_sce |
| DS analysis using mixed-models (MM) | .mm_dream .mm_dream2 .mm_glmm .mm_vst mmDS |
| pseudobulk DS analysis | pbDD pbDS |
| pbFlatten Flatten pseudobulk SCE | pbFlatten |
| Heatmap of cluster-sample pseudobulks | pbHeatmap |
| Pseudobulk-level MDS plot | pbMDS |
| Prepare SCE for DS analysis | prepSCE |
| SCE preparation for 'simData' | prepSim |
| resDS Formatting of DS analysis results | resDS |
| simData | simData |
| Perform two-stage testing on DS and DD analysis results | stagewise_DS_DD |
