valr-package | valr: genome interval arithmetic in R |
as.tbl_genome | Coerce objects to tbl_genome. |
as.tbl_genome.data.frame | Coerce objects to tbl_genome. |
as.tbl_genome.tbl_df | Coerce objects to tbl_genome. |
as.tbl_interval | Coerce objects to tbl_intervals. |
as.tbl_interval.data.frame | Coerce objects to tbl_intervals. |
as.tbl_interval.GRanges | Coerce objects to tbl_intervals. |
as.tbl_interval.tbl_df | Coerce objects to tbl_intervals. |
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_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 and statistics from overlapping intervals. |
bed_merge | Merge overlapping 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 tbl 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. |
concat | Calculate summaries and statistics 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. |
interval_spacing | Calculate interval spacing. |
is.tbl_genome | Test if the object is a tbl_genome. |
is.tbl_interval | Test if the object is a tbl_interval. |
read_bed | Read BED and related files. |
read_bed12 | Read BED and related files. |
read_bedgraph | Read BED and related files. |
read_broadpeak | Read BED and related files. |
read_genome | Read genome files. |
read_narrowpeak | Read BED and related files. |
read_vcf | Read a VCF file. |
tbl_genome | Tibble for reference sizes. |
tbl_interval | Tibble for intervals. |
trbl_genome | Tibble for reference sizes. |
trbl_interval | Tibble for intervals. |
valr | valr: genome interval arithmetic in R |
valr_example | Provide working directory for valr example files. |
values | Calculate summaries and statistics from overlapping intervals. |
values_unique | Calculate summaries and statistics from overlapping intervals. |