| Package Name | Access | Summary | Updated |
|---|---|---|---|
| faststructure | public | A variational framework for inferring population structure from SNP genotype data. | 2025-07-01 |
| r-exomedepth | public | Calls copy number variants (CNVs) from targeted sequence data, typically exome sequencing experiments designed to identify the genetic basis of Mendelian disorders. | 2025-06-30 |
| ucsc-facount | public | Count base statistics and CpGs in FA files. | 2025-06-30 |
| ucsc-headrest | public | Return all *but* the first N lines of a file. | 2025-06-30 |
| ucsc-mafcoverage | public | Analyse coverage by maf files - chromosome by. | 2025-06-30 |
| ucsc-ldhggene | public | Load database with gene predictions from a gff file. | 2025-06-30 |
| ucsc-splitfile | public | Split up a file. | 2025-06-30 |
| ucsc-hubcheck | public | Check a track data hub for integrity. | 2025-06-30 |
| ucsc-mafsplit | public | Split multiple alignment files. | 2025-06-30 |
| ucsc-catdir | public | Concatenate files in directory to stdout. | 2025-06-30 |
| ucsc-newprog | public | Make a new C source skeleton. | 2025-06-30 |
| ucsc-featurebits | public | Correlate tables via bitmap projections. | 2025-06-30 |
| ucsc-randomlines | public | Pick out random lines from file. | 2025-06-30 |
| ucsc-subchar | public | Substitute one character for another throughout a file. | 2025-06-30 |
| ucsc-genepredtofakepsl | public | Create a psl of fake-mRNA aligned to gene-preds from a file or table. | 2025-06-30 |
| ucsc-checkcoveragegaps | public | Check for biggest gap in coverage for a list of tracks. | 2025-06-30 |
| ucsc-estorient | public | Read ESTs from a database and determine orientation based on estOrientInfo table or direction in gbCdnaInfo table. Update PSLs so that the strand reflects the direction of transcription. By default, PSLs where the direction can't be determined are dropped. | 2025-06-30 |
| ucsc-mafspecieslist | public | Scan maf and output all species used in it. | 2025-06-30 |
| ucsc-qacagplift | public | Use AGP to combine per-scaffold qac into per-chrom qac. | 2025-06-30 |
| ucsc-countchars | public | Count the number of occurrences of a particular char. | 2025-06-30 |
| ucsc-netsyntenic | public | Add synteny info to net. | 2025-06-30 |
| ucsc-maftoaxt | public | Convert from maf to axt format. | 2025-06-30 |
| ucsc-blasttopsl | public | Convert blast alignments to PSLs. | 2025-06-30 |
| ucsc-bigwigcluster | public | Cluster bigWigs using a hacTree. | 2025-06-30 |
| ucsc-genepredhisto | public | Get data for generating histograms from a genePred file. | 2025-06-30 |
