Man pages for mdeber/BRGenomics
Tools for the Efficient Analysis of High-Resolution Genomics Data
| applyNFsGRanges | Apply normalization factors to GRanges object |
| binNdimensions | Generating and Aggregating Data Within N-dimensional Bins |
| bootstrap-signal-by-position | Bootstrapping Mean Signal by Position for Metaplotting |
| BRGenomics-package | BRGenomics: Tools for the Efficient Analysis of... |
| genebodies | Extract Genebodies |
| getCountsByPositions | Get signal counts at each position within regions of interest |
| getCountsByRegions | Get signal counts in regions of interest |
| getDESeqDataSet | Get DESeqDataSet objects for downstream analysis |
| getDESeqResults | Get DESeq2 results using reduced dispersion matrices |
| getMaxPositionsBySignal | Find sites with max signal in regions of interest |
| getPausingIndices | Calculate pausing indices from user-supplied promoters &... |
| getSpikeInCounts | Filtering and counting spike-in reads |
| getSpikeInNFs | Calculating spike-in normalization factors |
| getStrandedCoverage | Get strand-specific coverage |
| import_bam | Import bam files |
| import-functions | Import basepair-resolution files |
| intersectByGene | Intersect or reduce ranges according to gene names |
| makeGRangesBRG | Constructing and checking for base-pair resolution GRanges... |
| mergeGRangesData | Merge GRanges objects |
| mergeReplicates | Merge replicates of basepair-resolution GRanges objects |
| PROseq-data | PRO-seq data from Drosophila S2 cells |
| subsampleBySpikeIn | Randomly subsample reads according to spike-in normalization |
| subsampleGRanges | Randomly subsample reads from GRanges dataset |
| subsetRegionsBySignal | Subset regions of interest by quantiles of overlapping signal |
| tidyChromosomes | Remove odd chromosomes from GRanges objects |
| txs_dm6_chr4 | Ensembl transcripts for Drosophila melanogaster, dm6,... |
