| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-axttopsl | public | Convert axt to psl format. | 2025-06-28 |
| ucsc-chaintoaxt | public | Convert from chain to axt file. | 2025-06-28 |
| ucsc-chainantirepeat | public | Get rid of chains that are primarily the results of repeats and degenerate DNA. | 2025-06-28 |
| ucsc-bedgeneparts | public | Given a bed, spit out promoter, first exon, or all introns. | 2025-06-28 |
| ucsc-bedrestricttopositions | public | Filter bed file, restricting to only ones that match chrom/start/ends specified in restrict.bed file. | 2025-06-28 |
| ucsc-bigmaftomaf | public | Convert bigMaf to maf file. | 2025-06-28 |
| ucsc-chaintopslbasic | public | Basic conversion chain file to psl format. | 2025-06-28 |
| ucsc-beditemoverlapcount | public | Count number of times a base is overlapped by the items in a bed file. | 2025-06-28 |
| ucsc-bedremoveoverlap | public | Remove overlapping records from a (sorted) bed file. | 2025-06-28 |
| ucsc-bigwigcat | public | Merge non-overlapping bigWig files. | 2025-06-28 |
| ucsc-bigbednameditems | public | Extract item of given name from bigBed. | 2025-06-28 |
| ucsc-chainfilter | public | Filter chain files. Output goes to standard out. | 2025-06-28 |
| ucsc-chainnet | public | Make alignment nets out of chains. | 2025-06-28 |
| ucsc-bedpileups | public | Find (exact) overlaps if any in bed input. | 2025-06-28 |
| ucsc-bigpsltopsl | public | Convert bigPsl file to psl. | 2025-06-28 |
| ucsc-bedintersect | public | Intersect two bed files. | 2025-06-28 |
| ucsc-chainmergesort | public | Combine sorted files into larger sorted file. | 2025-06-28 |
| ucsc-bedcoverage | public | Analyse coverage by bed files - chromosome by chromosome and genome-wide. | 2025-06-28 |
| ucsc-lavtoaxt | public | Convert blastz lav file to an axt file (which includes sequence). | 2025-06-28 |
| ucsc-checkagpandfa | public | Takes a .agp file and .fa file and ensures that they are in synch. | 2025-06-28 |
| ucsc-bedweedoverlapping | public | Filter out beds that overlap a 'weed.bed' file. | 2025-06-28 |
| ucsc-chaintopsl | public | Convert chain file to psl format. | 2025-06-28 |
| ucsc-chainsplit | public | Split chains up by target or query sequence. | 2025-06-28 |
| ucsc-bedcommonregions | public | Create a bed file (just bed3) that contains the regions common to all inputs. | 2025-06-28 |
| ucsc-chainstitchid | public | Join chain fragments with the same chain ID into a single chain per ID. | 2025-06-28 |
