| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-autosql | public | Create SQL and C code for permanently storing. | 2025-06-28 |
| ucsc-autodtd | public | Give this a XML document to look at and it will come up with a DTD. | 2025-06-28 |
| ucsc-axtsort | public | Sort axt files. | 2025-06-28 |
| ucsc-axtswap | public | Swap source and query in an axt file. | 2025-06-28 |
| ucsc-axttomaf | public | Convert from axt to maf format. | 2025-06-28 |
| ucsc-autoxml | public | Generate structures code and parser for XML file from DTD-like spec. | 2025-06-28 |
| 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 |
