Man pages for timoast/signac
Analysis of Single-Cell Chromatin Data
| AccessiblePeaks | Accessible peaks |
| AddChromatinModule | Add chromatin module |
| AddMotifs | Add DNA sequence motif information |
| AggregateTiles | Quantify aggregated genome tiles |
| AlleleFreq | Compute allele frequencies per cell |
| Annotation | Annotation |
| AnnotationPlot | Plot gene annotations |
| as.ChromatinAssay | Convert objects to a ChromatinAssay |
| atac_small | A small example scATAC-seq dataset |
| AverageCounts | Average Counts |
| BigwigTrack | Plot data from BigWig files |
| BinarizeCounts | Binarize counts |
| blacklist_ce10 | Genomic blacklist regions for C. elegans ce10 (0-based) |
| blacklist_ce11 | Genomic blacklist regions for C. elegans ce11 (0-based) |
| blacklist_dm3 | Genomic blacklist regions for Drosophila dm3 (0-based) |
| blacklist_dm6 | Genomic blacklist regions for Drosophila dm6 (0-based) |
| blacklist_hg19 | Genomic blacklist regions for Human hg19 (0-based) |
| blacklist_hg38 | Genomic blacklist regions for Human GRCh38 |
| blacklist_hg38_unified | Unified genomic blacklist regions for Human GRCh38 |
| blacklist_mm10 | Genomic blacklist regions for Mouse mm10 (0-based) |
| CallPeaks | Call peaks |
| Cells | Set and get cell barcode information for a 'Fragment' object |
| CellsPerGroup | Cells per group |
| Cells-set | Set and get cell barcode information for a Fragment object |
| ChromatinAssay-class | The ChromatinAssay class |
| ClosestFeature | Closest Feature |
| ClusterClonotypes | Find relationships between clonotypes |
| CombineTracks | Combine genome region plots |
| ConnectionsToLinks | Cicero connections to links |
| ConvertMotifID | Convert between motif name and motif ID |
| corSparse | Sparse matrix correlation |
| CountFragments | Count fragments |
| CountsInRegion | Counts in region |
| CoverageBrowser | Genome browser |
| coverage-ChromatinAssay-method | Coverage of a ChromatinAssay object |
| CoveragePlot | Plot Tn5 insertion frequency over a region |
| CreateChromatinAssay | Create ChromatinAssay object |
| CreateFragmentObject | Create a Fragment object |
| CreateMotifMatrix | Create motif matrix |
| CreateMotifObject | Create motif object |
| DensityScatter | Scatterplot colored by point density |
| DepthCor | Plot sequencing depth correlation |
| DownsampleFeatures | Downsample Features |
| ExpressionPlot | Plot gene expression |
| Extend | Extend |
| FeatureMatrix | Feature Matrix |
| FilterCells | Filter cells from fragment file |
| FindClonotypes | Find clonotypes |
| FindMotifs | FindMotifs |
| findOverlaps-methods | Find overlapping ranges for ChromatinAssay objects |
| FindTopFeatures | Find most frequently observed features |
| Footprint | Transcription factor footprinting analysis |
| FractionCountsInRegion | Fraction of counts in a genomic region |
| Fragment-class | The Fragment class |
| FragmentHistogram | Plot fragment length histogram |
| Fragments | Get the Fragment objects |
| FRiP | Calculate fraction of reads in peaks per cell |
| GeneActivity | Create gene activity matrix |
| GenomeBinMatrix | Genome bin matrix |
| GetCellsInRegion | Get cells in a region |
| GetFootprintData | Get footprinting data |
| GetFragmentData | Get Fragment object data |
| GetGRangesFromEnsDb | Extract genomic ranges from EnsDb object |
| GetIntersectingFeatures | Find intersecting regions between two objects |
| GetLinkedGenes | Get genes linked to peaks |
| GetLinkedPeaks | Get peaks linked to genes |
| GetMotifData | Retrieve a motif matrix |
| GetTSSPositions | Find transcriptional start sites |
| granges-methods | Access genomic ranges for ChromatinAssay objects |
| GRangesToString | GRanges to String |
| head.Fragment | Return the first rows of a fragment file |
| IdentifyVariants | Identify mitochondrial variants |
| InsertionBias | Compute Tn5 insertion bias |
| inter-range-methods | Inter-range transformations for ChromatinAssay objects |
| IntersectMatrix | Intersect genomic coordinates with matrix rows |
| Jaccard | Calculate the Jaccard index between two matrices |
| LinkPeaks | Link peaks to genes |
| LinkPlot | Plot linked genomic elements |
| Links | Get or set links information |
| LookupGeneCoords | Get gene coordinates |
| MatchRegionStats | Match DNA sequence characteristics |
| Motif-class | The Motif class |
| MotifCounts | Count fragments surrounding motif sites |
| MotifPlot | Plot DNA sequence motif |
| Motifs | Get or set a motif information |
| nearest-methods | Find the nearest range neighbors for ChromatinAssay objects |
| NucleosomeSignal | NucleosomeSignal |
| PeakPlot | Plot peaks in a genomic region |
| PlotFootprint | Plot motif footprinting results |
| ReadMGATK | Read MGATK output |
| reexports | Objects exported from other packages |
| RegionHeatmap | Region heatmap |
| RegionMatrix | Region enrichment analysis |
| RegionPlot | Region plot |
| RegionStats | Compute base composition information for genomic ranges |
| RunChromVAR | Run chromVAR |
| RunSVD | Run singular value decomposition |
| RunTFIDF | Compute the term-frequency inverse-document-frequency |
| seqinfo-methods | Access and modify sequence information for ChromatinAssay... |
| SetMotifData | Set motif data |
| Signac-package | Signac: Analysis of Single-Cell Chromatin Data |
| SortIdents | Sorts cell metadata variable by similarity using hierarchical... |
| SplitFragments | Split fragment file by cell identities |
| StringToGRanges | String to GRanges |
| subset.Fragment | Subset a Fragment object |
| SubsetMatrix | Subset matrix rows and columns |
| subset.Motif | Subset a Motif object |
| theme_browser | Genome browser theme |
| TilePlot | Plot integration sites per cell |
| TSSEnrichment | Compute TSS enrichment score per cell |
| TSSPlot | Plot signal enrichment around TSSs |
| UnifyPeaks | Unify genomic ranges |
| UpdatePath | Update the file path for a Fragment object |
| ValidateCells | Validate cells present in fragment file |
| ValidateFragments | Validate Fragment object |
| ValidateHash | Validate hashes for Fragment object |
| VariantPlot | Plot strand concordance vs. VMR |
