| Package Name | Access | Summary | Updated |
|---|---|---|---|
| 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 |
| ucsc-bedtopsl | public | Convert bed format files to psl format. | 2025-06-28 |
| ucsc-hgloadsqltab | public | Load table into database from SQL and text files. | 2025-06-28 |
| ucsc-hgloadwiggle | public | Load a wiggle track definition into database. | 2025-06-28 |
| ucsc-bedgraphpack | public | Pack together adjacent records representing same value. | 2025-06-28 |
| ucsc-bedextendranges | public | Extend length of entries in bed 6+ data to be at least the given length, taking strand directionality into account. | 2025-06-28 |
| ucsc-chainswap | public | Swap target and query in chain. | 2025-06-28 |
| dwgsim | public | Whole Genome Simulator for Next-Generation Sequencing | 2025-06-27 |
| starcode | public | Starcode: sequence clustering based on all-pairs search | 2025-06-27 |
| bioconductor-missmethyl | public | Analysing Illumina HumanMethylation BeadChip Data | 2025-06-27 |
| ucsc-twobitdup | public | check to see if a twobit file has any identical sequences in it | 2025-06-27 |
| ucsc-xmltosql | public | Convert XML dump into a fairly normalized relational database. | 2025-06-27 |
| ucsc-twobitmask | public | Apply masking to a .2bit file, creating a new .2bit file. | 2025-06-27 |
| ucsc-wigcorrelate | public | Produce a table that correlates all pairs of wigs. | 2025-06-27 |
| ucsc-validatemanifest | public | Validates the ENCODE3 manifest.txt file. | 2025-06-27 |
| ucsc-toupper | public | Convert lower case to upper case in file. Leave other chars alone. | 2025-06-27 |
| ucsc-validatefiles | public | Validates the format of different genomic files. | 2025-06-27 |
| ucsc-trfbig | public | Mask tandem repeats on a big sequence file. | 2025-06-27 |
| ucsc-transmappsltogenepred | public | Convert PSL alignments of mRNAs to gene annotations. | 2025-06-27 |
| ucsc-wordline | public | Chop up words by white space and output them with one. | 2025-06-27 |
