Bug fixes:
macs2 exists at themacs2.pathinCallPeaks() (#1678)LinkPeaks() that incorrectly excludedadditional chromosomes from background peak setOther changes:
seqinfo links from documentation asfunctions are moved fromGenomeInfoDb toSeqinfowrswoR package is installedwrswoR to suggested packagesMatchRegionStats() to use likelihood-ratioweighting (query/background probability) to sample regions. Thisproduces more accurate matching distributions between query andbackground features. This change will affect how background peaks areselected for theFindMotifs() andLinkPeaks()functions.New features:
group.order parameter toRegionPlot() andRegionHeatmap() functions tocontrol order of plotted groups (#1745)Bug fixes:
RegionMatrix() positionenrichment information is present in the object.RegionPlot() x-axis (Other changes:
FindMotifs() (#1788)FeatureMatrix() to return asmany rows as input granges (New features:
SortIdents() function to automatically order cellmetadata according to similarity (Other changes:
CoverageBrowser()ClosestFeature() whengene annotations are not present in the object (#1681)CreateChromatinAssay() when supplying apre-computed Motif object (#1657)CoveragePlot() when combiningcells andgroup.by parameters (#1724)FeatureMatrix() when requestedfeatures are on seqnames not present in the fragment file (#1754)Bug fixes:
SetAssayData() forChromatinAssay objects (#1538)TSSEnrichment() causing error on smallexample dataset (#1563)Footprint() when running on a small numberof regions (#1614)CoveragePlot() andPlotFootprint() when setting bothident andsplit.by parameters (#1660)MatchRegionStats() when NA values arepresent in only some of the feature metadata rows (#1655)Other changes:
CoveragePlot() (#1459)corSparse(), remove qlcMatrix from suggestedpackages (#1570)GetLinkedPeaks() andGetLinkedGenes() (#1654)Bug fixes:
FilterCells()(#1509)Other changes:
Bug fixes:
AddMotifs()function (#1437)Other changes:
region_extension parameter toTSSEnrichment() function to enable changing the size of theregion used to compute TSS enrichment scores (#1444;New functionality:
DensityScatter() functionscale.linewidth parameter toLinkPlot() (#1412)Bug fixes:
GetReadsInRegion() when no fragmentspresent that overlap the region (BigwigTrack() (#1389)RegionMatrix() where regions on minusstrand were not handled correctly (#1368)Other changes:
AddMotifs() function (#1361)Bug fixes:
CoveragePlot() when settingshow.bulk=TRUE (#1294)Other changes:
tol parameter toRunSVD() to controltheirlba::irlba()tol parametersplit.by parameters toCoveragePlot() andPlotFootprint() (#523)Bug fixes:
FeatureMatrix() where cell names would notbe converted correctly when running withcells=NULL (#1198)Other changes:
subset() method forFragment-classobjectsCoverageTrack to enablereproducible coverage plots (#1206)PeakPlot(),LinkPlot(), andAnnotationPlot() (#919)Motif class definition to allow anyCsparseMatrix in the data slotNew functionality:
method parameter toLinkPeaks() (annotation="transcript" inCoveragePlot())FindMotifs(), andnewp.adjust column in output dataframep.adjust.method parameter toFindMotifs() to control multiple testing correction methodusedBug fixes:
CallPeaks() when project name containedwhitespace (#981)CoveragePlot() whentile=TRUEInsertionBias() that set the coordinatesbeyond the end of some chromosomes (#986)BigwigTrack() when supplying a singlebigwig file (#1053)GeneActivity() when specifying biotypes(#1058)GeneActivity() when gene name is an emptystring (#1055)FeatureMatrix() when using list ofFragment objects (#1056)RegionMatrix() when running on objectscontaining renamed cells (#1076)Footprint() when using a FASTA file (#1092)Footprint() when using list of genomicregions (#1098)FindMotifs() (#1109)Other changes:
CallPeaks() (#1062)Seurat,ggforce,ggrepel,ggseqlogo,lsa,qlcMatrix to suggested packagesGetGRangesFromEnsDb()New functionality:
RegionHeatmap() functionRegionPlot() functionRegionMatrix() functionMotifCounts() functionCoveragePlot() by providing a list of assay namesassay.scale,bigwig.scale, andsplit.assay parameters toCoveragePlot()ymax value inCoveragePlot()bigwig.scale andymax parameters toBigwigTrack()peak.slot parameter toLinkPeaks()(#932)Bug fixes:
min.features parameter inCreateChromatinAssay() to retain cells with>= min.features (#902)min.cells parameter inLinkPeaks() (#932)Other changes:
Bug fixes:
FeatureMatrix() when cells information notpresent in Fragment object (#803)LinkPeaks() using Ensembl IDs (#858)GeneActivity() when gene names areNA (#865)FeatureMatrix() when only one regionsuppliedExpressionPlot() when usingscaled data (#893)Other changes:
idf parameter toRunTFIDF() to useprecomputed IDF vectorgene.id parameter toGeneActivity()to allow output genes named using gene ID (#837)sep parameter toConnectionsToLinks() (#841)New functionality:
CoveragePlot(). Theassay parameter can now bea list of assays to plot data from, with signal colored by assay oforigin.Bug fixes:
FindMotifs() when using only one region asinput (#732)ClosestFeature() when query containedregions on contigs not present in gene annotation (#758)TSSEnrichment() when using multiplefragment files (#783)CallPeaks() when multiple fragment filesused as inputCallPeaks() to account for 0-based startsin called peaks-characters (#759)Other changes:
genome parameter inAddMotifs() andRunChromVAR() (#712)FoldChange() function to use normalizedcounts rather than raw counts (#795)GeneActivity() (#797)format parameter toCallPeaks() (#682)Bug fixes:
LinkPeaks() function when running on a singlegene (#629)fragment.tempdir parameter toCallPeaks() to enable setting directory that split fragmentfiles are written to during peak calling (#579)FeatureMatrix() when settingsep parameter (#626)RenameCells() when cell informationnot present in Fragment object (#704)Other changes:
GeneActivity() (#625)FoldChange() method forChromatinAssay() object that sets proper parameters forchromatin data. This fixes the calculation of fold changes when runningSeurat::FindMarkers() on single-cell chromatin data.New functionality:
head() method forFragment-classobjects.Bug fixes:
ChromatinAssay merging (#596)Other changes:
New functionality:
BigwigTrack() function to plot data from bigWigfilesbigwig andbigwig.type arguments toCoveragePlot() to include bigWig files inCoveragePlot()region.highlight parameter toCoveragePlot()biotypes parameter toGeneActivity()andGetTSSPositions() functionsmax.width parameter toGeneActivity()min.distance parameter toLinkPeaks() (#561)Bug fixes:
standard.chromosomes parameter inGetGRangesFromEnsDb() (#513)group.by parameter inPlotFootprint() (#522)GeneActivity() to be incorrect (#521)FindMotifs() (#549)CountsInRegion() (#563)Other changes:
TSSEnrichment() (#485)ChromatinAssay-specific functions onnon-ChromatinAssay assaysn inNucleosomeSignal()TSSEnrichment() whenfast=TRUELinkPeaks() (#550)LinkPeaks() (#550)biovizBase andBiostrings tosuggested packagesggbio dependencyAnnotationPlot()New functionality:
group.by parameter toPeakPlot() toallow coloring plotted genomic ranges by metadata variables.peaks.group.by andranges.group.byparameters toCoveragePlot() to allow coloring plottedgenomic ranges inCoveragePlot() to be colored by metadatavariables.Bug fixes:
assay parameter inCoveragePlot()CreateChromatinAssay() (#387)CreateChromatinAssay() when setting bothmin.cells andmin.features arguments (#390)PlotFootprint() when only one cell in anidentity class (#406)Other changes:
SeuratObject dependencyNew functionality:
CallPeaks() function to call peaks using MACS2.Peaks can be called for different groups of cells separately by settingthegroup.by parameterLinkPeaks() function to link peaks to correlatedgenes.AddMotifs() function to add motif information toa Seurat object or ChromatinAssay.AggregateTiles() function to combine adjacentgenome tilesranges parameter toCoveragePlot()to plot addition sets of genomic rangesshow.bulk parameter toCoveragePlot() to plot accessibility of all cellscombinedFragment objects and modify thefile path for existing fragment objects (#206)Bug fixes:
AlleleFreq() (#196 and#260)FeatureMatrix() (#205,#291)CreateChromatinAssay() when settingmin.features argument (#194)CreateChromatinAssay() when settingmin.cells argument (#292)TSSEnrichment() when cell information notset for fragment files (#203)TSSEnrichment() when no fragments presentin TSS region (#244)qvalue calculation fromFindMotifs() (#223)SetAssayData() when setting thescale.data slotOther changes:
MatchRegionStats()function when matching distribution of multiple features (eg, GC contentand overall accessibility)MatchRegionStats()This release includes major updates to the Signac package, includingnew functionality, performance improvements, and new datastructures.
The entire package has been updated to use the newChromatinAssay class for the storage of single-cellchromatin data. This is an extension of the standard SeuratAssay that adds additional slots needed for the analysis ofchromatin data, including genomic ranges, genome information, fragmentfile information, motifs, gene annotations, and genomic links.
In addition, we have defined a newFragment class tostore information relating to a fragment file. This makes use of thefragment files within Signac more robust, as checks are now performed toverify that the expected cells are present in the fragment file, andthat the fragment file or index are not modified on disk.
Key new functionality:
http orftp.Footprint() andPlotFootprint() functions forTF footprinting analysis.granges(),findOverlaps(),seqinfo(), and otherBioconductor generic functions directly on theChromatinAssay orSeurat object.CoveragePlot() function.CoverageBrowser()function.Other changes:
NucleosomeSignal(): we have greatly improvedthe scalability ofNucleosomeSignal(), and fixed a bugpresent in previous versions. The score computed byNucleosomeSignal() in 1.0.0 will be different to thatcomputed by previous versions of Signac.CountFragments() function: a fast, memory-efficientfunction implemented in C++ that counts the total number of fragmentsfor each cell barcode present in a fragment file.fast option in theTSSEnrichment()function. Setting this toTRUE will compute the TSSenrichment score per cell without storing the entire cell by TSSposition matrix. This can significantly reduce memory requirements forlarge datasets, but does not allow subsequent plotting of the TSS signalfor different groups of cells.TilePlot() function andtile parameterforCoveragePlot() to plot Tn5 integration events in agenomic region for individual cells.FeatureMatrix(),CoveragePlot(), andTSSEnrichment()blacklist_hg38_unified object.FRiP() function to use total fragmentcounts per cell stored in object metadata.DepthCor function to compute the correlationbetween sequencing depth and reduced dimension components.RunTFIDF.ClosestFeaturesandCoveragePlot. Use GRanges instead.ucsc parameter fromCoveragePlot.nchunk was greater than the number offeatures used.CoveragePlot that would prevent plottingmultiple regions when usingGRanges.CoveragePlot that would prevent plottingwhen a different assay was active.SubsetMatrix function to subset a matrix based onnumber of non-zero elements in the rows or columns.seed.use parameter fromRunSVD.UnifyPeaks function to create a merged set of peaksfrom multiple samples.RunSVD: previously, scaling was applied toeach cell rather than each component. Now, mean centering and SD scalingare applied to the cell embeddings within a component.scale.embeddings option toRunSVD tocontrol whether embeddings are scaled and centered.irlba.work parameter toRunSVD.SingleCoveragePlot from exported functionsRunSVDCoveragePlotCoveragePlotPeriodPlot toFragmentHistogramneighbors andreductions slotsfrommotif classmotif.names slot tomotif classCoveragePlotGRangesobjectCoveragePlotFilterFragmentsGetCellsInRegionTSSEnrichment andTSSPlot functionsfor TSS enrichment scoringInsertionBias functionCoveragePlot for scaling tracksCoveragePlotCoveragePlot: now plots a Tn5 integrationscore per base, rather than the whole fragment.GetIntersectingFeatures function to findoverlapping peaks between objectsMergeWithRegions function to perform region-awareSeurat object mergingRunChromVAR function to run chromVAR throughSignacRegionStats function to add statistics about peaksequences to the feature metadataFindMotifs: now selects a set ofbackground peaks matching the sequence characteristics of the inputIntersectMatrixChunkGRanges