valr-package |
valr: genome interval arithmetic in R |
bed12_to_exons |
Convert BED12 to individual exons in BED6. |
bed_absdist |
Compute absolute distances between intervals. |
bed_closest |
Identify closest intervals. |
bed_cluster |
Cluster neighboring intervals. |
bed_complement |
Identify intervals in a genome not covered by a query. |
bed_coverage |
Compute coverage of intervals. |
bed_fisher |
Fisher's test to measure overlap between two sets of intervals. |
bed_flank |
Create flanking intervals from input intervals. |
bed_genomecov |
Calculate coverage across a genome |
bed_glyph |
Create example glyphs for valr functions. |
bed_intersect |
Identify intersecting intervals. |
bed_jaccard |
Calculate the Jaccard statistic for two sets of intervals. |
bed_makewindows |
Divide intervals into new sub-intervals ("windows"). |
bed_map |
Calculate summaries from overlapping intervals. |
bed_merge |
Merge overlapping intervals. |
bed_partition |
Partition intervals into elemental intervals |
bed_projection |
Projection test for query interval overlap. |
bed_random |
Generate randomly placed intervals on a genome. |
bed_reldist |
Compute relative distances between intervals. |
bed_shift |
Adjust intervals by a fixed size. |
bed_shuffle |
Shuffle input intervals. |
bed_slop |
Increase the size of input intervals. |
bed_sort |
Sort a set of intervals. |
bed_subtract |
Subtract two sets of intervals. |
bed_window |
Identify intervals within a specified distance. |
bound_intervals |
Select intervals bounded by a genome. |
check_genome |
Bed-like data.frame requirements for valr functions |
check_interval |
Bed-like data.frame requirements for valr functions |
concat |
Calculate summaries from overlapping intervals. |
create_introns |
Create intron features. |
create_tss |
Create transcription start site features. |
create_utrs3 |
Create 3' UTR features. |
create_utrs5 |
Create 5' UTR features. |
db |
Fetch data from remote databases. |
db_ensembl |
Fetch data from remote databases. |
db_ucsc |
Fetch data from remote databases. |
flip_strands |
Flip strands in intervals. |
genome_df |
Bed-like data.frame requirements for valr functions |
gr_to_bed |
Convert Granges to bed tibble |
interval_spacing |
Calculate interval spacing. |
ivl_df |
Bed-like data.frame requirements for valr functions |
read_bed |
Read BED and related files. |
read_bed12 |
Read BED and related files. |
read_bedgraph |
Read BED and related files. |
read_bigwig |
Import and convert a bigwig file into a valr compatible tbl |
read_broadpeak |
Read BED and related files. |
read_genome |
Read genome files. |
read_gtf |
Import and convert a GTF/GFF file into a valr compatible bed tbl format |
read_narrowpeak |
Read BED and related files. |
read_vcf |
Read a VCF file. |
valr |
valr: genome interval arithmetic in R |
valr_example |
Provide working directory for valr example files. |
values |
Calculate summaries from overlapping intervals. |
values_unique |
Calculate summaries from overlapping intervals. |