Files in r3fang/SnapATAC
Single Nucleus Analysis Package for ATAC-Seq
.Rbuildignore
.gitignore
DESCRIPTION
LICENSE
NAMESPACE
R/createGmat.R
R/createPmat.R
R/data.R
R/dimReduct-class.R
R/findDARs.R
R/jaccard-class.R
R/kgraph-class.R
R/makeBinary.R
R/normJaccard.R
R/plottings-utilities.R
R/plottings.R
R/predictGenePeakPair.R
R/runChromVAR.R
R/runClusters.R
R/runDimReduct.R
R/runHarmony.R
R/runHomer.R
R/runJaccard.R
R/runKNN.R
R/runLDA.R
R/runLDM.R
R/runLSA.R
R/runMACS.R
R/runMagic.R
R/runSnapAddPmat.R
R/runViz.R
R/scaleCountMatrix.R
R/snap-class.R
R/snap-utilities.R
R/snapToSeurat.R
R/utilities.R
README.md
SnapATAC.Rproj
data/demo.sp.rda
examples/10X_PBMC_15K/BinCovDist.png
examples/10X_PBMC_15K/DARs.png
examples/10X_PBMC_15K/IGV_track.png
examples/10X_PBMC_15K/QualityControl1.png
examples/10X_PBMC_15K/QualityControl2.png
examples/10X_PBMC_15K/README.md
examples/10X_PBMC_15K/Viz_UMAP.png
examples/10X_PBMC_15K/Viz_umap_type.png
examples/10X_PBMC_15K/arc_plot.png
examples/10X_PBMC_15K/diff_plot_CD14+_Monocytes.png
examples/10X_PBMC_15K/eigs_scatter_plot.png
examples/10X_PBMC_15K/gene_exp_plot.png
examples/10X_PBMC_15K/motif_homer_plot.png
examples/10X_PBMC_15K/motif_var_plot.png
examples/10X_PBMC_15K/predict_score.png
examples/10X_brain_5k/BinCovDist.png
examples/10X_brain_5k/DARs.png
examples/10X_brain_5k/DARs_all.png
examples/10X_brain_5k/QualityControl.png
examples/10X_brain_5k/README.md
examples/10X_brain_5k/Visulization.png
examples/10X_brain_5k/Visulization_tree.png
examples/10X_brain_5k/Visulization_tsne.png
examples/10X_brain_5k/chromVAR_2B.png
examples/10X_brain_5k/chromVAR_2C.png
examples/10X_brain_5k/cluster_tree.png
examples/10X_brain_5k/eigs_scatter_plot.png
examples/10X_brain_5k/gene_plot.png
examples/10X_brain_5k/homer_motif.pdf
examples/10X_brain_5k/homer_motif.png
examples/10X_snATAC/.DS_Store
examples/10X_snATAC/README.md
examples/10X_snATAC/eigs_scatter_plot.png
examples/10X_snATAC/intro.png
examples/10X_snATAC/viz.png
examples/10X_snATAC/viz2.png
images/10X_brain_5k.png
images/10X_sci.png
images/10X_snATAC.png
images/PBMC_ATAC_RNA.png
images/SnapATAC_intro.gif
inst/extdata/demo.snap
man/addBmatToSnap.Rd
man/addGmatToSnap.Rd
man/addPmatToSnap.Rd
man/barcodeInSnapFile.Rd
man/boxPlotFeature.Rd
man/calBmatCor.Rd
man/colMeans-methods.Rd
man/colSums-methods.Rd
man/createGmatFromMat.Rd
man/createPmat.Rd
man/createSnap.Rd
man/createSnapFromBmat.Rd
man/createSnapFromGmat.Rd
man/createSnapFromPmat.Rd
man/demo.sp.Rd
man/dim.reduct-class.Rd
man/exportMetaData.Rd
man/extractReads.Rd
man/filterBins.Rd
man/filterCells.Rd
man/findDAR.Rd
man/is.snap-methods.Rd
man/isSnapFile.Rd
man/jaccard-class.Rd
man/kgraph-class.Rd
man/makeBinary.Rd
man/newSnap.Rd
man/nrow-methods.Rd
man/plotBarcode.Rd
man/plotBinCoverage.Rd
man/plotDimReductElbow.Rd
man/plotDimReductPW.Rd
man/plotFeatureSingle.Rd
man/plotGene.Rd
man/plotViz.Rd
man/predictGenePeakPair.Rd
man/readMetaData.Rd
man/rmBmatFromSnap.Rd
man/rmGmatFromSnap.Rd
man/rmPmatFromSnap.Rd
man/rowMeans-methods.Rd
man/rowSums-methods.Rd
man/runChromVAR.Rd
man/runCluster.Rd
man/runDiffusionMaps.Rd
man/runDiffusionMapsExtension.Rd
man/runDimReduct.Rd
man/runHarmony.Rd
man/runHomer.Rd
man/runJaccard.Rd
man/runKNN.Rd
man/runLDA.Rd
man/runLSA.Rd
man/runMACS.Rd
man/runMACSForAll.Rd
man/runMagic.Rd
man/runNormJaccard.Rd
man/runSnapAddPmat.Rd
man/runViz.Rd
man/scaleCountMatrix.Rd
man/showBinSizes.Rd
man/snap-class.Rd
man/snapRbind.Rd
man/snapToSeurat.Rd
man/sub-dim.reduct-ANY-ANY-ANY-method.Rd
man/sub-jaccard-ANY-ANY-ANY-method.Rd
man/sub-kgraph-ANY-ANY-ANY-method.Rd
man/sub-snap-ANY-ANY-ANY-method.Rd
man/summarySnap-methods.Rd
notebooks/experiemnt_timeline.md
notebooks/experiemnt_timeline.png
