| Package Name | Access | Summary | Updated |
|---|---|---|---|
| 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 |
| flexbar | public | Flexible barcode and adapter removal | 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 |
| 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-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 |
| ucsc-ixixx | public | Create indices for simple line-oriented file of format. | 2025-06-26 |
| ucsc-bigwiginfo | public | Print out information about bigWig file. | 2025-06-26 |
| ucsc-bigwigtobedgraph | public | Convert from bigWig to bedGraph format. | 2025-06-26 |
| ucsc-gff3togenepred | public | Convert a GFF3 file to a genePred file. | 2025-06-26 |
| ucsc-pslcheck | public | Validate PSL files. | 2025-06-25 |
| ucsc-nibfrag | public | Extract part of a nib file as .fa (all bases/gaps lower case by default). | 2025-06-25 |
| ucsc-bigwigtowig | public | Convert bigWig to wig. This will keep more of the same structure of the original wig than bigWigToBedGraph does, but still will break up large stepped sections into smaller ones. | 2025-06-25 |
| crossmap | public | CrossMap is a program for convenient conversion of genome coordinates and genomeannotation files between assemblies. | 2025-06-25 |
