Man pages for Honchkrow/SignacSlim
The slim version of signac
| AggregateTiles | Quantify aggregated genome tiles |
| AlleleFreq | Compute allele frequencies per cell |
| Annotation | Annotation |
| ApplyMatrixByGroup | Apply function to integration sites per base per group |
| as.ChromatinAssay | Convert objects to a ChromatinAssay |
| Assay-class | The Assay Class |
| BinarizeCounts | Binarize counts |
| Cells | Set and get cell barcode information for a 'Fragment' object |
| Cells-set | Set and get cell barcode information for a Fragment object |
| ChromatinAssay-class | The ChromatinAssay class |
| ChunkGRanges | Split a genomic ranges object into evenly sized chunks |
| CountFragments | Count fragments |
| coverage-ChromatinAssay-method | Coverage of a ChromatinAssay object |
| CreateChromatinAssay | Create ChromatinAssay object |
| CreateFragmentObject | Create a Fragment object |
| CreateRegionPileupMatrix | Create cut site pileup matrix |
| DimReduc-class | The DimReduc Class |
| Extend | Extend |
| ExtractCell | Extract cell |
| ExtractFragments | Run groupCommand for the first n lines, convert the cell... |
| FeatureMatrix | Construct a feature x cell matrix from a genomic fragments... |
| FilterCells | Filter cells from fragment file |
| findOverlaps-methods | Find overlapping ranges for ChromatinAssay objects |
| Fragment-class | The Fragment class |
| FragmentHistogram | Plot fragment length histogram |
| Fragments | Get the Fragment objects |
| GetAssay | Get an Assay object from a given Seurat object. |
| GetCellsInRegion | Get cells in a region |
| GetFragmentData | Get Fragment object data |
| GetGRangesFromEnsDb | Extract genomic ranges from EnsDb object |
| GetGroups | Get vector of cell names and associated identity |
| GetTSSPositions | Find transcriptional start sites |
| granges-methods | Access genomic ranges for ChromatinAssay objects |
| GRangesToString | GRanges to String |
| Graph-class | The Graph Class |
| head.Fragment | Return the first rows of a fragment file |
| inter-range-methods | Inter-range transformations for ChromatinAssay objects |
| isRemote | Check if path is remote |
| JackStrawData-class | The JackStrawData Class |
| Links | Get or set links information |
| nearest-methods | Find the nearest range neighbors for ChromatinAssay objects |
| Neighbor-class | The Neighbor Class |
| NucleosomeSignal | NucleosomeSignal |
| Read10X_h5 | Read 10X hdf5 file |
| reexports | Objects exported from other packages |
| RegionMatrix | Region enrichment analysis |
| RegionStats | Compute base composition information for genomic ranges |
| seqinfo-methods | Access and modify sequence information for ChromatinAssay... |
| SetIfNull | Set a default value if an object is null |
| Seurat-class | The Seurat Class |
| SeuratCommand-class | The SeuratCommand Class |
| SingleFeatureMatrix | Run FeatureMatrix on a single Fragment object |
| SpatialImage-class | The SpatialImage Class |
| SplitFragments | Split fragment file by cell identities |
| StringToGRanges | String to GRanges |
| TSSEnrichment | Compute TSS enrichment score per cell |
| TSSPlot | Plot signal enrichment around TSSs |
| UpdatePath | Update the file path for a Fragment object |
| UpdateSlots | Update slots in an object |
| ValidateCells | Validate cells present in fragment file |
| ValidateFragments | Validate Fragment object |
| ValidateHash | Validate hashes for Fragment object |
