| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-pslprottornacoords | public | Convert protein alignments to RNA coordinates. | 2025-06-26 |
| ucsc-pslsplicejunctions | public | Extract splice junctions from a PSL file. | 2025-06-26 |
| fasta_ushuffle | public | a wrapper for uShuffle | 2025-06-26 |
| ucsc-hggcpercent | public | Calculate GC Percentage in 20kb windows. | 2025-06-26 |
| ucsc-genepredtobiggenepred | public | Converts genePred or genePredExt to bigGenePred input (bed format with extra fields). | 2025-06-26 |
| ucsc-genepredcheck | public | Validate genePred files or tables. | 2025-06-26 |
| ucsc-bigbedtobed | public | Convert from bigBed to ascii bed format. | 2025-06-26 |
| binette | public | A fast and accurate binning refinement tool to constructs high quality MAGs from the output of multiple binning tools. | 2025-06-26 |
| flexbar | public | Flexible barcode and adapter removal | 2025-06-26 |
| rpbp | public | Ribosome profiling with Bayesian predictions (Rp-Bp) | 2025-06-26 |
| r-bascule | public | Bayesian inference and clustering of mutational signatures leveraging biological priors | 2025-06-26 |
| famseq | public | Peng G, Fan Y, Palculict TB, Shen P, Ruteshouser EC, Chi A, Davis RW, Huff V, Scharfe C, Wang W. Rare variant detection using family-based sequencing analysis. Proceedings of the National Academy of Sciences. 2013 Mar 5;110(10):3985-90 | 2025-06-26 |
| expansionhunterdenovo | public | ExpansionHunter Denovo (EHdn) is a suite of tools for detecting novel expansions of short tandem repeats (STRs). | 2025-06-26 |
| ucsc-genepredtogtf | public | Convert genePred table or file to gtf. | 2025-06-26 |
| ucsc-fatrans | public | Translate DNA .fa file to peptide. | 2025-06-26 |
| ucsc-oligomatch | public | find perfect matches in sequence. | 2025-06-26 |
| ucsc-pslpostarget | public | flip psl strands so target is positive and implicit | 2025-06-26 |
| ucsc-gaptolift | public | Create lift file from gap table(s). | 2025-06-26 |
| ucsc-psltochain | public | Convert psl records to chain records. | 2025-06-26 |
| ucsc-psltobed | public | Transform a psl format file to a bed format file. | 2025-06-26 |
| ucsc-pslsort | public | Merge and sort psCluster .psl output files. | 2025-06-26 |
| ucsc-pslsortacc | public | Remove chain-breaking alignments from chains that break nested chains. | 2025-06-26 |
| ucsc-pslstats | public | Collect statistics from a psl file. | 2025-06-26 |
| ucsc-pslpairs | public | Join paired ends in psl alignments. | 2025-06-26 |
| ucsc-qactowig | public | Convert from compressed quality score format to wiggle format. | 2025-06-26 |
