| Package Name | Access | Summary | Updated |
|---|---|---|---|
| saffrontree | public | No Summary | 2025-07-07 |
| chromhmm | public | ChromHMM is software for learning and characterizing chromatin states. ChromHMM can integrate multiple chromatin datasets such as ChIP-seq data of various histone modifications to discover de novo the major re-occuring combinatorial and spatial patterns of marks. | 2025-07-07 |
| perl-cgi | public | A generic file fetching mechanism. | 2025-07-07 |
| ls-gkm | public | gkm-SVM, a sequence-based method for predicting regulatory DNA elements. | 2025-07-03 |
| repeatmodeler | public | RepeatModeler is a de-novo repeat family identification and modeling package. | 2025-07-03 |
| domclust | public | Effective tool for orthologous grouping in multiple genomes | 2025-07-03 |
| beast | public | BEAST is a cross-platform program for Bayesian analysis of molecular sequences using MCMC. | 2025-07-03 |
| primer3-py | public | Python bindings for Primer3 | 2025-07-02 |
| r-lme4qtl | public | Linear mixed models (lme4) with flexible covariance structure for qtl and association analysis. | 2025-07-02 |
| ucsc-overlapselect | public | Select records based on overlapping chromosome ranges. | 2025-07-02 |
| 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 |
