Files in beyondpie/smmtools
Single-cell multi-omics sequenceing data tools
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
LICENSE.md
NAMESPACE
R/AnnotationGenome.R
R/BatchCorrection.R
R/Clustering.R
R/ColorPalettes.R
R/DimReduction.R
R/Doublet.R
R/FeatureFilter.R
R/GeneMatrix.R
R/IntegrateATACWithRNA.R
R/QualityControl.R
R/RcppExports.R
R/Tabix.R
R/TileMatrix.R
R/Utility.R
R/Visualization.R
R/ggplotUtils.R
R/scATACCNV.R
README.Rmd
README.md
data/ArchRgeneAnnoHg19.rda
data/ArchRgeneAnnoHg19test.rda
data/ArchRgeneAnnoHg38.rda
data/ArchRgeneAnnoMm10.rda
data/ArchRgeneAnnoMm9.rda
data/ArchRgenomeAnnoHg19.rda
data/ArchRgenomeAnnoHg19test.rda
data/ArchRgenomeAnnoHg38.rda
data/ArchRgenomeAnnoMm10.rda
data/ArchRgenomeAnnoMm9.rda
data/gencode.vM16.geneUp2k.bed
data/gencode.vM16.geneUp2k.binarystr.bed
data/mm10.blacklist.bed
data/mm10.chrom.sizes
eval/GeneMatrix.R
eval/geneMatrix.py
eval/makefile
eval/test_getHarmonyMatrix.R
eval/with_SnapATAC.R
inst/rscript/SnapATAC_QC_filter.R
inst/rscript/SnapATAC_pre_stat.R
inst/rscript/filterBarcodesByScrubletDoublet.R
inst/rscript/filterBarcodesFromQC.R
inst/rscript/getGmat.R
inst/rscript/getScrubletDoublet.R
inst/rscript/getSumFragment.R
inst/rscript/getTabixToH5.R
inst/rscript/plotScrubletScores.R
inst/smmuty/MANIFEST.in
inst/smmuty/README.md
inst/smmuty/bin/generate_genome_bins.py
inst/smmuty/bin/map_snap_to_genomebins.py
inst/smmuty/pyproject.toml
inst/smmuty/setup.py
inst/smmuty/smmuty/__init__.py
inst/smmuty/smmuty/doublet.py
inst/smmuty/smmuty/genome.py
inst/smmuty/smmuty/leiden.py
inst/smmuty/smmuty/snaptools.py
makefile
man/ArchRPalettes.Rd
man/SnapATACPalette.Rd
man/SnapATAC_BinarizeBmat.Rd
man/SnapATAC_DiffusionMaps.Rd
man/SnapATAC_runDiffusionMaps.Rd
man/SnapATAC_runDiffusionMapsExtension.Rd
man/SnapATAC_runHarmony.Rd
man/SnapATAC_runScrublet.Rd
man/cleanOutfile.Rd
man/eig_decomp.Rd
man/fastGetTSSEnrichmentSingleThread.Rd
man/fastH5Read.Rd
man/filterChrGR.Rd
man/getAnnotFromArchRData.Rd
man/getBlacklist.Rd
man/getBmatFromSnap.Rd
man/getFragsOfAChrFromRawH5File.Rd
man/getGeneMatrix.Rd
man/getGmatFromSnap.Rd
man/getIndex.Rd
man/getNfragmentPerBarcode.Rd
man/getNormOVE.Rd
man/getScrubletThresholdByMixEM.Rd
man/getTSSFromTxDb.Rd
man/getTileMatrix.Rd
man/getiFromSparseMatrix.Rd
man/getjFromSparseMatrix.Rd
man/getvalFromSparseMatrix.Rd
man/ggPoint.Rd
man/installGenomeRelatedDatabase.Rd
man/loadBmatFromFile.Rd
man/loadGeneMatrix.Rd
man/loadSnapATACGmatFromFile.Rd
man/loadSparseMatrixFromMatTextFile.Rd
man/loadTileMatrix.Rd
man/paletteContinuous.Rd
man/paletteDiscrete.Rd
man/plotDimReductElbow.Rd
man/plotDimReductPairwise.Rd
man/plot_scATAC_cnv.Rd
man/readColumnsFromTextFile.Rd
man/removeSampleName.Rd
man/runJaccard2.Rd
man/runKNN.Rd
man/runLeiden.Rd
man/runUMAP.Rd
man/sampleBasedOnDepth.Rd
man/sampleBasedOnDepth2.Rd
man/simplifyGRSeqnames.Rd
man/snapGmat2Seurat.Rd
man/subsetGeneAnnoByGenomeAnno.Rd
man/subsetSeqnamesGR.Rd
man/sumFragmentSingleThread.Rd
man/suppressAll.Rd
man/t.sparseMatrix.Rd
man/tabixToH5SingleThread.Rd
man/theme_ArchR.Rd
man/tileChrom.Rd
src/.gitignore
src/RcppExports.cpp
src/Utils.cpp
tests/testthat.R
tests/testthat/test-IntegrateATACWithRNA.R
tests/testthat/testdata/testMouseBrainOrgSeurat.rds
tests/testthat/testdata/testSnap.rds
