| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-netchainsubset | public | Create chain file with subset of chains that appear in the net. | 2025-06-29 |
| ucsc-faonerecord | public | Extract a single record from a .FA file. | 2025-06-29 |
| ucsc-mafspeciessubset | public | Extract a maf that just has a subset of species. | 2025-06-29 |
| ucsc-hgloadoutjoined | public | Load new style (2014) RepeatMasker .out files into database. | 2025-06-29 |
| ucsc-genepredtoprot | public | Create protein sequences by translating gene annotations. | 2025-06-29 |
| ucsc-findmotif | public | Find specified motif in sequence. | 2025-06-29 |
| ucsc-fafilter | public | Filter fa records, selecting ones that match the specified conditions. | 2025-06-29 |
| ucsc-ticktodate | public | Convert seconds since 1970 to time and date. | 2025-06-29 |
| ucsc-hgloadout | public | Load RepeatMasker .out files into database. | 2025-06-29 |
| ucsc-faalign | public | Align two fasta files. | 2025-06-29 |
| ucsc-maskoutfa | public | Produce a masked .fa file given an unmasked .fa and. | 2025-06-29 |
| cnvkit | public | Copy number variant detection from high-throughput sequencing. | 2025-06-29 |
| bioconductor-dmrcate | public | Methylation array and sequencing spatial analysis methods | 2025-06-29 |
| ucsc-fafrag | public | Extract a piece of DNA from a .fa file. | 2025-06-29 |
| ucsc-maffetch | public | Get overlapping records from an MAF using an index table. | 2025-06-29 |
| ucsc-gmtime | public | Convert unix timestamp to date string. | 2025-06-29 |
| ucsc-chainsort | public | Sort chains. By default sorts by score. | 2025-06-29 |
| ucsc-maketablelist | public | Create/recreate tableList tables (cache of SHOW TABLES and DESCRIBE). | 2025-06-29 |
| ucsc-maffilter | public | Filter out maf files. Output goes to standard out. | 2025-06-29 |
| ucsc-hgloadnet | public | Load a generic net file into database. | 2025-06-29 |
| ucsc-bigwigmerge | public | Merge together multiple bigWigs into a single output bedGraph. | 2025-06-29 |
| ucsc-hubpubliccheck | public | Checks that the labels in hubPublic match what is in the hub labels. | 2025-06-29 |
| ucsc-maffrag | public | Extract maf sequences for a region from database. | 2025-06-29 |
| ucsc-hgfindspec | public | Create hgFindSpec table from trackDb.ra files. | 2025-06-29 |
| ucsc-chainprenet | public | Remove chains that don't have a chance of being netted. | 2025-06-29 |
