| Package Name | Access | Summary | Updated |
|---|---|---|---|
| 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 |
| oarfish | public | oarfish is a tool for fast, accurate and versatile transcript quantification from long-read RNA-seq data | 2025-06-29 |
| r-restfulr | public | Models a RESTful service as if it were a nested R list. | 2025-06-28 |
| ucsc-pslswap | public | Swap target and query in psls. | 2025-06-28 |
| reactome-cli | public | Reactome CLI bioconda | 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 |
| 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 |
