All functions

GenomicDistributions

Produces summaries and plots of features distributed across genomes

TSSDistance()

Calculates the distribution of distances from a query set to closest TSS

TSS_hg19

TSS locations

TSS_hg38

TSS locations

TSS_mm10

TSS locations

TSS_mm9

TSS locations

aggregateOverGenomeBins()

Returns the distribution of query over a reference assembly Given a query set of elements (a GRanges object) and a reference assembly (*e.g. 'hg38'), this will aggregate and count the distribution of the query elements across bins of the reference genome

assignPartitions()

Takes a GRanges object, then assigns each element to a partition from the provided partitionList, and then tallies the number of regions assigned to each partition. A typical example of partitions is promoter, exon, intron, etc; this function will yield the number of each for a query GRanges object There will be a priority order to these, to account for regions that may overlap multiple genomic partitions.

binBSGenome()

Bins a BSgenome object.

binChroms()

Naively splits a chromosome into bins

binRegion()

Divide regions into roughly equal bins

chromSizes_hg19

Chromosome sizes

chromSizes_hg38

Chromosome sizes

chromSizes_mm10

Chromosome sizes

chromSizes_mm9

Chromosome sizes

featureAggregateDistribution()

Calculates the distribution of a query set over the genome

featureDistanceDistribution()

Find the distance to the nearest genomic feature

geneModels_hg19

Gene models

geneModels_hg38

Gene models

geneModels_mm10

Gene models

geneModels_mm9

Gene models

genomePartitionList()

Create a basic genome partition list of genes, exons, introns, and intergenic

genomicPartitions()

Calculates the distribution of overlaps for a query set to genomic partitions

loadBSgenome()

Loads BSgenome objects from UCSC-style character vectors.

loadEnsDb()

Loads Ensemble gene annotations (EnsDb objects) from UCSC-style character vectors

plotFeatureDist()

Plots a histogram of distances to genomic features

plotGenomeAggregate()

Plot distribution over chromosomes

plotPartitions()

Produces a barplot showing how query regions of interest are distributed across a given partition list