| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-netsplit | public | Split a genome net file into chromosome net files. | 2025-06-29 |
| ucsc-mafaddqrows | public | Add quality data to a maf. | 2025-06-29 |
| ucsc-fastqtofa | public | Convert from fastq to fasta format. | 2025-06-29 |
| ucsc-crtreeindexbed | public | Create an index for a bed file. | 2025-06-29 |
| ucsc-liftup | public | Change coordinates of .psl, .agp, .gap, .gl, .out, .align, .gff, .gtf. | 2025-06-29 |
| ucsc-hgtrackdb | public | Create trackDb table from text files. | 2025-06-29 |
| ucsc-fafiltern | public | Get rid of sequences with too many N's. | 2025-06-29 |
| ucsc-rasqlquery | public | Do a SQL-like query on a RA file. | 2025-06-29 |
| 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 |
