| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-pslhisto | public | Collect counts on PSL alignments for making histograms. These then be analyzed with R, textHistogram, etc. | 2025-06-28 |
| ucsc-pslsomerecords | public | Extract multiple psl records. | 2025-06-28 |
| ucsc-pslmap | public | Map PSLs alignments to new targets using alignments of the old target to the new target. | 2025-06-28 |
| ucsc-pslliftsubrangeblat | public | Lift PSLs from blat subrange alignments. | 2025-06-28 |
| ucsc-pslrc | public | Reverse-complement psl. | 2025-06-28 |
| ucsc-addcols | public | Sum columns in a text file. | 2025-06-28 |
| ucsc-ameme | public | Find common patterns in DNA. | 2025-06-28 |
| ucsc-bamtopsl | public | Convert a bam file to a psl and optionally also a fasta file that contains the reads. | 2025-06-28 |
| ucsc-avecols | public | Average together columns. | 2025-06-28 |
| ucsc-axtchain | public | Chain together axt alignments. | 2025-06-28 |
| 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 |
