Man pages for databio/GenomicDistributions
GenomicDistributions: fast analysis of genomic intervals with Bioconductor
| binBSGenome | Bins a BSgenome object. |
| binChroms | Naively splits a chromosome into bins |
| binRegion | Divide regions into roughly equal bins |
| BSdtToGRanges | Converts a list of data.tables (From BSreadbeds) into... |
| calcChromBins | Calculates the distribution of a query set over the genome |
| calcChromBinsRef | Returns the distribution of query over a reference assembly... |
| calcChromBinsRefSlow | Returns the distribution of query over a reference assembly... |
| calcCumulativePartitions | Calculates the cumulative distribution of overlaps between... |
| calcCumulativePartitionsRef | Calculates the cumulative distribution of overlaps for a... |
| calcDinuclFreq | Calculate Dinuclotide content over genomic ranges |
| calcDinuclFreqRef | Calculate dinucleotide content over genomic ranges |
| calcExpectedPartitions | Calculates expected partiton overlap based on contribution of... |
| calcExpectedPartitionsRef | Calculates the distribution of observed versus expected... |
| calcFeatureDist | Find the distance to the nearest genomic feature |
| calcFeatureDistRefTSS | Calculates the distribution of distances from a query set to... |
| calcGCContent | Calculate GC content over genomic ranges |
| calcGCContentRef | Calculate GC content over genomic ranges |
| calcNearestNeighbors | Group regions from the same chromosome together and compute... |
| calcNeighborDist | Group regions from the same chromosome together and calculate... |
| calcPartitions | Calculates the distribution of overlaps between query and... |
| calcPartitionsRef | Calculates the distribution of overlaps for a query set to a... |
| calcSummarySignal | The function calcSummarySignal takes the input BED file(s) in... |
| calcWidth | Calculate the widths of regions |
| cellTypeMetadata | Table the maps cell types to tissues and groups |
| chromSizes_hg19 | hg19 chromosome sizes |
| dot-requireAndReturn | Checks to make sure a package object is installed, and if so,... |
| dot-validateInputs | Checks class of the list of variables. To be used in... |
| dtToGr | Converts a data.table (DT) object to a GenomicRanges (GR)... |
| dtToGrInternal | Two utility functions for converting data.tables into GRanges... |
| exampleOpenSignalMatrix_hg19 | A dataset containing a subset of open chromatin regions... |
| geneModels_hg19 | hg38 gene models |
| genomePartitionList | Create a basic genome partition list of genes, exons,... |
| GenomicDistributions | Produces summaries and plots of features distributed across... |
| getChromSizes | Returns built-in chrom sizes for a given reference assembly |
| getChromSizesFromFasta | Get gene models from a remote or local FASTA file |
| getGeneModels | Returns built-in gene models for a given reference assembly |
| getGeneModelsFromGTF | Get gene models from a remote or local GTF file |
| getGenomeBins | Returns bins used in 'calcChromBins' function Given a named... |
| getReferenceData | Get reference data for a specified assembly |
| getTssFromGTF | Get transcription start sites (TSSs) from a remote or local... |
| grToDt | Convert a GenomicRanges into a data.table. |
| labelCuts | Creates labels based on a discretization definition. |
| loadBSgenome | Loads BSgenome objects from UCSC-style character vectors. |
| loadEnsDb | Load selected EnsDb library |
| neighbordt | Internal helper function to calculate distance between... |
| nlist | Nathan's magical named list function. This function is a... |
| plotChromBins | Plot distribution over chromosomes |
| plotCumulativePartitions | Plot the cumulative distribution of regions in features |
| plotDinuclFreq | Plot dinuclotide content within region set(s) |
| plotExpectedPartitions | Produces a barplot showing how query regions of interest are... |
| plotFeatureDist | Plots a histogram of distances to genomic features |
| plotGCContent | Plots a density distribution of GC vectors Give results from... |
| plotNeighborDist | Plot the distances from regions to their upstream/downstream... |
| plotPartitions | Produces a barplot showing how query regions of interest are... |
| plotQTHist | Plot quantile-trimmed histogram |
| plotSummarySignal | The function plotSummarySignal visualizes the... |
| retrieveFile | Read local or remote file |
| setB_100 | Example BED file read with rtracklayer::import |
| splitDataTable | Efficiently split a data.table by a column in the table |
| theme_blank_facet_label | Clear ggplot face label. |
| TSS_hg19 | hg19 TSS locations |
| vistaEnhancers | Example BED file read with rtracklayer::import |
