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Signac  

Analysis of Single-Cell Chromatin Data
View on CRAN: Click here


Download and install Signac package within the R console
Install from CRAN:
install.packages("Signac")

Install from Github:
library("remotes")
install_github("cran/Signac")

Install by package version:
library("remotes")
install_version("Signac", "1.13.0")



Attach the package and use:
library("Signac")
Maintained by
Tim Stuart
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2020-03-13
Latest Update: 2023-11-08
Description:
A framework for the analysis and exploration of single-cell chromatin data. The 'Signac' package contains functions for quantifying single-cell chromatin data, computing per-cell quality control metrics, dimension reduction and normalization, visualization, and DNA sequence motif analysis. Reference: Stuart et al. (2021) <doi:10.1038/s41592-021-01282-5>.
How to cite:
Tim Stuart (2020). Signac: Analysis of Single-Cell Chromatin Data. R package version 1.13.0, https://cran.r-project.org/web/packages/Signac
Previous versions and publish date:
0.2.4 (2020-03-13 09:50), 0.2.5 (2020-04-16 11:10), 1.0.0 (2020-08-16 17:50), 1.1.0 (2020-11-07 01:20), 1.1.1 (2021-02-04 00:50), 1.2.0 (2021-04-28 19:30), 1.2.1 (2021-05-11 16:22), 1.3.0 (2021-07-12 15:00), 1.4.0 (2021-09-22 13:50), 1.5.0 (2021-12-08 18:40), 1.6.0 (2022-03-05 15:30), 1.7.0 (2022-06-01 15:00), 1.8.0 (2022-09-21 20:20), 1.9.0 (2022-12-08 18:02), 1.10.0 (2023-05-30 10:50), 1.11.0 (2023-10-13 06:20), 1.12.0 (2023-11-08 10:30)
Other packages that cited Signac R package
View Signac citation profile
Other R packages that Signac depends, imports, suggests or enhances
Functions, R codes and Examples using the Signac R package
Some associated functions: AccessiblePeaks . AddChromatinModule . AddMotifs . AggregateTiles . AlleleFreq . Annotation . AnnotationPlot . AverageCounts . BigwigTrack . BinarizeCounts . CallPeaks . Cells-set . Cells . CellsPerGroup . ChromatinAssay-class . ClosestFeature . ClusterClonotypes . CombineTracks . ConnectionsToLinks . ConvertMotifID . CountFragments . CountsInRegion . CoverageBrowser . CoveragePlot . CreateChromatinAssay . CreateFragmentObject . CreateMotifMatrix . CreateMotifObject . DepthCor . DownsampleFeatures . ExpressionPlot . Extend . FRiP . FeatureMatrix . FilterCells . FindClonotypes . FindMotifs . FindTopFeatures . Footprint . FractionCountsInRegion . Fragment-class . FragmentHistogram . Fragments . GRangesToString . GeneActivity . GenomeBinMatrix . GetCellsInRegion . GetFootprintData . GetFragmentData . GetGRangesFromEnsDb . GetIntersectingFeatures . GetLinkedGenes . GetLinkedPeaks . GetMotifData . GetTSSPositions . IdentifyVariants . InsertionBias . IntersectMatrix . Jaccard . LinkPeaks . LinkPlot . Links . LookupGeneCoords . MatchRegionStats . Motif-class . MotifCounts . MotifPlot . Motifs . NucleosomeSignal . PeakPlot . PlotFootprint . ReadMGATK . RegionHeatmap . RegionMatrix . RegionPlot . RegionStats . RunChromVAR . RunSVD . RunTFIDF . SetMotifData . Signac-package . SplitFragments . StringToGRanges . SubsetMatrix . TSSEnrichment . TSSPlot . TilePlot . UnifyPeaks . UpdatePath . ValidateCells . ValidateFragments . ValidateHash . VariantPlot . as.ChromatinAssay . atac_small . blacklist_ce10 . blacklist_ce11 . blacklist_dm3 . blacklist_dm6 . blacklist_hg19 . blacklist_hg38 . blacklist_hg38_unified . blacklist_mm10 . coverage-ChromatinAssay-method . findOverlaps-methods . granges-methods . head.Fragment . inter-range-methods . nearest-methods . reexports . seqinfo-methods . subset.Fragment . subset.Motif . theme_browser . 
Some associated R codes: RcppExports.R . data.R . differential_accessibility.R . dimension_reduction.R . footprinting.R . fragments.R . generics.R . genomeinfodb-methods.R . granges-methods.R . heatmaps.R . iranges-methods.R . links.R . mito.R . motifs.R . objects.R . peaks.R . preprocessing.R . quantification.R . region-enrichment.R . utilities.R . visualization.R . zzz.R .  Full Signac package functions and examples
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