Files in timoast/signac

Analysis of Single-Cell Chromatin Data

.github/CODE_OF_CONDUCT.md .github/ISSUE_TEMPLATE/--documentation.md .github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature-request.md CONTRIBUTING.md LICENSE.md NEWS.md R/RcppExports.R R/data.R R/differential_accessibility.R R/dimension_reduction.R R/footprinting.R R/fragments.R R/generics.R R/genomeinfodb-methods.R R/granges-methods.R R/heatmaps.R R/iranges-methods.R R/links.R R/mito.R R/motifs.R R/objects.R R/peaks.R R/preprocessing.R R/quantification.R R/region-enrichment.R R/utilities.R R/visualization.R R/zzz.R README.md index.md man/AccessiblePeaks.Rd man/AddChromatinModule.Rd man/AddMotifs.Rd man/AggregateTiles.Rd man/AlleleFreq.Rd man/Annotation.Rd man/AnnotationPlot.Rd man/AverageCounts.Rd man/BigwigTrack.Rd man/BinarizeCounts.Rd man/CallPeaks.Rd man/Cells-set.Rd man/Cells.Rd man/CellsPerGroup.Rd man/ChromatinAssay-class.Rd man/ClosestFeature.Rd man/ClusterClonotypes.Rd man/CombineTracks.Rd man/ConnectionsToLinks.Rd man/ConvertMotifID.Rd man/CountFragments.Rd man/CountsInRegion.Rd man/CoverageBrowser.Rd man/CoveragePlot.Rd man/CreateChromatinAssay.Rd man/CreateFragmentObject.Rd man/CreateMotifMatrix.Rd man/CreateMotifObject.Rd man/DensityScatter.Rd man/DepthCor.Rd man/DownsampleFeatures.Rd man/ExpressionPlot.Rd man/Extend.Rd man/FRiP.Rd man/FeatureMatrix.Rd man/FilterCells.Rd man/FindClonotypes.Rd man/FindMotifs.Rd man/FindTopFeatures.Rd man/Footprint.Rd man/FractionCountsInRegion.Rd man/Fragment-class.Rd man/FragmentHistogram.Rd man/Fragments.Rd man/GRangesToString.Rd man/GeneActivity.Rd man/GenomeBinMatrix.Rd man/GetCellsInRegion.Rd man/GetFootprintData.Rd man/GetFragmentData.Rd man/GetGRangesFromEnsDb.Rd man/GetIntersectingFeatures.Rd man/GetLinkedGenes.Rd man/GetLinkedPeaks.Rd man/GetMotifData.Rd man/GetTSSPositions.Rd man/IdentifyVariants.Rd man/InsertionBias.Rd man/IntersectMatrix.Rd man/Jaccard.Rd man/LinkPeaks.Rd man/LinkPlot.Rd man/Links.Rd man/LookupGeneCoords.Rd man/MatchRegionStats.Rd man/Motif-class.Rd man/MotifCounts.Rd man/MotifPlot.Rd man/Motifs.Rd man/NucleosomeSignal.Rd man/PeakPlot.Rd man/PlotFootprint.Rd man/ReadMGATK.Rd man/RegionHeatmap.Rd man/RegionMatrix.Rd man/RegionPlot.Rd man/RegionStats.Rd man/RunChromVAR.Rd man/RunSVD.Rd man/RunTFIDF.Rd man/SetMotifData.Rd man/Signac-package.Rd man/SortIdents.Rd man/SplitFragments.Rd man/StringToGRanges.Rd man/SubsetMatrix.Rd man/TSSEnrichment.Rd man/TSSPlot.Rd man/TilePlot.Rd man/UnifyPeaks.Rd man/UpdatePath.Rd man/ValidateCells.Rd man/ValidateFragments.Rd man/ValidateHash.Rd man/VariantPlot.Rd man/as.ChromatinAssay.Rd man/atac_small.Rd man/blacklist_ce10.Rd man/blacklist_ce11.Rd man/blacklist_dm3.Rd man/blacklist_dm6.Rd man/blacklist_hg19.Rd man/blacklist_hg38.Rd man/blacklist_hg38_unified.Rd man/blacklist_mm10.Rd man/corSparse.Rd man/coverage-ChromatinAssay-method.Rd man/findOverlaps-methods.Rd man/granges-methods.Rd man/head.Fragment.Rd man/inter-range-methods.Rd man/nearest-methods.Rd man/reexports.Rd man/seqinfo-methods.Rd man/subset.Fragment.Rd man/subset.Motif.Rd man/theme_browser.Rd tests/testthat.R tests/testthat/test-dimreduc.R tests/testthat/test-mito.R tests/testthat/test-preprocessing.R tests/testthat/test-utilities.R tests/testthat/test_fragments.R vignettes/archive.Rmd vignettes/cicero.Rmd vignettes/data_structures.Rmd vignettes/faq.Rmd vignettes/footprint.Rmd vignettes/future.Rmd vignettes/install.Rmd vignettes/integrate_atac.Rmd vignettes/merging.Rmd vignettes/mito.Rmd vignettes/monocle.Rmd vignettes/motif_vignette.Rmd vignettes/mouse_brain_vignette.Rmd vignettes/overview.Rmd vignettes/pbmc_multiomic.Rmd vignettes/pbmc_vignette.Rmd vignettes/peak_calling.Rmd vignettes/snareseq.Rmd vignettes/visualization.Rmd