Man pages for steveped/chipExtra
Additional functions for working with ChIP-Seq data
| addDiffStatus-methods | Add a status column |
| as_tibble | Convert to a tibble |
| bestOverlap-methods | Find the best overlap between GRanges |
| centrePeaks-methods | Re-estimate peak centres from coverage |
| chopMC | Keep unique ranges and collapse mcols |
| collapseGenes | Collapse a vector of gene names |
| colToRanges-methods | Coerce a column to a GRanges object |
| cytobands | Cytogenetic bands |
| defineRegions | Define Genomic Regions Based on Gene Annotations |
| defineSeqinfo | Use package data to define a Seqinfo object |
| distinctMC | Keep distinct ranges and mcols |
| dot-makeFinalProfileHeatmap | Make a profile heatmap |
| dot-mapFeatures | Map ranges to genes using features as an anchor |
| dot-mapGi | Map ranges to genes via Interactions |
| dot-mapWithin | Map ranges to all genes within a set distance |
| dualFilter | Apply two filters to sliding windows |
| ex_datasets | Datasets for an example region |
| extraChIPs-package | extraChIPs: A package for enabling and extending ChIP-Seq... |
| fitAssayDiff-methods | Detect Differential ChIP Signal |
| fixed_width_datasets | Datasets for the Fixed-Width Vignette |
| getProfileData-methods | Get Profile Data surrounding specified ranges |
| grlToSE-methods | Set columns from a GRangesList as Assays in a... |
| importPeaks | Import peaks |
| makeConsensus | Make a set of consensus peaks |
| mapByFeature | Map Genomic Ranges to genes using defined features |
| mapGrlCols | Collapse a GRangesList adding multiple columns from each... |
| mergeByCol-methods | Merge sliding windows using a specified column |
| mergeByHMP-methods | Merge Sliding Windows using the Harmonic Mean P |
| mergeBySig-methods | Merge overlapping ranges based on p-values |
| partitionRanges-methods | Partition a set of Genomic Ranges |
| plotAssayDensities-methods | Plot Densities for any assay within a SummarizedExperiment |
| plotAssayHeatmap-methods | Draw a heatmap from a single SummarizedExperiment assay |
| plotAssayPCA-methods | Plot PCA For any assay within a SummarizedExperiment |
| plotAssayRle-methods | Plot RLE for a given assay within a SummarizedExperiment |
| plotGrlCol | Draw a plot from a GRangesList column |
| plotHFGC | Plot a Genomic Region showing HiC, Features, Genes and... |
| plotOverlaps-methods | Plot Overlaps Between List Elements |
| plotPairwise | Plot Pairwise Values from a GRangeList |
| plotPie-methods | Draw Pie Graphs based on one or more columns |
| plotProfileHeatmap-methods | Draw a coverage Profile Heatmap |
| plotSplitDonut-methods | Draw Two-Level Donut Charts |
| propOverlap-methods | Find the proportions of an overlapping range |
| reduceMC | Reduce ranges retaining mcols |
| setoptsMC-methods | Perform set operations retaining mcols |
| stitchRanges | Stitch Ranges within a given distance |
| voomWeightsFromCPM | Estimate voom precision weights directly From CPM values |
