| Package Name | Access | Summary | Updated |
|---|---|---|---|
| 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 |
| ucsc-pslfilter | public | Filter out psl file. | 2025-06-28 |
| ucsc-psldropoverlap | public | Deletes all overlapping self alignments. | 2025-06-28 |
| ucsc-parafetch | public | Try to fetch url with multiple connections. | 2025-06-28 |
| ucsc-psltopslx | public | Convert from psl to pslx format, which includes sequences. | 2025-06-28 |
| ucsc-pslpartition | public | Split PSL files into non-overlapping sets. | 2025-06-28 |
| ucsc-pslrecalcmatch | public | Recalculate match, mismatch, repMatch columns in psl file. | 2025-06-28 |
| ucsc-pslpretty | public | Convert PSL to human-readable output. | 2025-06-28 |
| ucsc-positionaltblcheck | public | Check that positional tables are sorted. | 2025-06-28 |
| ucsc-pslmappostchain | public | Post genomic pslMap (TransMap) chaining. This takes transcripts that have been mapped via genomic chains adds back in blocks that didn't get include in genomic chains due to complex rearrangements or other issues. | 2025-06-28 |
| 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 |
