| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-mafsinregion | public | Extract MAFS in a genomic region. | 2025-06-29 |
| ucsc-mafsplitpos | public | Pick positions to split multiple alignment input files. | 2025-06-29 |
| ucsc-taillines | public | Add tail to each line of file. | 2025-06-29 |
| ucsc-hgloadchain | public | Load a generic Chain file into database. | 2025-06-29 |
| ucsc-mafranges | public | Extract ranges of target (or query) coverage from maf and. | 2025-06-29 |
| ucsc-chromgraphfrombin | public | Convert chromGraph binary to ascii format. | 2025-06-29 |
| ucsc-getrnapred | public | Get virtual RNA for gene predictions. | 2025-06-29 |
| ucsc-catuncomment | public | Concatenate input removing lines that start with '#'. | 2025-06-29 |
| ucsc-chopfalines | public | Read in FA file with long lines and rewrite it with shorter lines. | 2025-06-29 |
| ucsc-hgsqldump | public | Execute mysqldump using passwords from .hg.conf. | 2025-06-29 |
| ucsc-hgloadmaf | public | Load a maf file index into the database. | 2025-06-29 |
| ucsc-getrna | public | Get mrna for GenBank or RefSeq sequences found in a database. | 2025-06-29 |
| ucsc-texthistogram | public | Make a histogram in ascii. | 2025-06-29 |
| ucsc-gff3topsl | public | Convert a GFF3 CIGAR file to a PSL file. | 2025-06-29 |
| ucsc-maftobigmaf | public | Put ucsc standard maf file into bigMaf format. | 2025-06-29 |
| ucsc-mrnatogene | public | Convert PSL alignments of mRNAs to gene annotations. | 2025-06-29 |
| ucsc-genepredtomafframes | public | Create mafFrames tables from a genePreds. | 2025-06-29 |
| ucsc-genepredsinglecover | public | Create single-coverage genePred files. | 2025-06-29 |
| ucsc-pslswap | public | Swap target and query in psls. | 2025-06-28 |
| ucsc-pslmrnacover | public | Make histogram of coverage percentage of mRNA in psl. | 2025-06-28 |
| ucsc-pslcat | public | Concatenate psl files. | 2025-06-28 |
| ucsc-pslreps | public | Analyze repeats and generate genome-wide best alignments from a sorted set of local alignments. | 2025-06-28 |
| ucsc-pslscore | public | Calculate web blat score from psl files. | 2025-06-28 |
| ucsc-pslselect | public | Select records from a PSL file. | 2025-06-28 |
| ucsc-pslxtofa | public | Convert pslx (with sequence) to fasta file. | 2025-06-28 |
