| Package Name | Access | Summary | Updated |
|---|---|---|---|
| ucsc-tolower | public | Convert upper case to lower case in file. Leave other chars alone. | 2025-06-27 |
| last | public | LAST finds & aligns related regions of sequences. | 2025-06-27 |
| blastbesties | public | Rapid discovery of reciprocal best blast pairs from BLAST output files. | 2025-06-27 |
| masurca | public | MaSuRCA (Maryland Super-Read Celera Assembler) genome assembly software. | 2025-06-26 |
| ucsc-bigwigaverageoverbed | public | Compute average score of big wig over each bed, which may have introns. | 2025-06-26 |
| ucsc-bedsort | public | Sort a .bed file by chrom,chromStart. | 2025-06-26 |
| ucsc-xmlcat | public | Concatenate xml files together, stuffing all records inside a single outer tag. | 2025-06-26 |
| ucsc-bigbedsummary | public | Extract summary information from a bigBed file. | 2025-06-26 |
| ucsc-bigbedinfo | public | Show information about a bigBed file. | 2025-06-26 |
| ucsc-bedclip | public | Remove lines from bed file that refer to off-chromosome locations. | 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 |
| 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 |
