| Package Name | Access | Summary | Updated |
|---|---|---|---|
| shortstack | public | ShortStack: Comprehensive annotation and quantification of small RNA genes | 2025-05-24 |
| pyseer | public | Sequence Element Enrichment Analysis (SEER), python implementation. | 2025-05-22 |
| ucsc-cell-browser | public | A browser for single-cell data, main site at http://cells.ucsc.edu. UCSC Cellbrowser, an interactive browser for single cell data. Includes importers and basic pipelines for text files, Seurat, Scanpy and Cellranger. All Javascript - does not require a server backend. | 2025-05-22 |
| meme | public | Motif-based sequence analysis tools. | 2025-05-20 |
| vcflib | public | Command-line tools for manipulating VCF files. | 2025-05-19 |
| bamtools | public | C++ API & command-line toolkit for working with BAM data. | 2025-05-18 |
| perl-vcftools-vcf | public | cpanm ready distribution of VCFtools Perl libraries | 2025-05-15 |
| vcftools | public | A set of tools written in Perl and C++ for working with VCF files. | 2025-05-15 |
| picrust2 | public | PICRUSt: Phylogenetic Investigation of Communities by Reconstruction of Unobserved States | 2025-05-14 |
| fido | public | No Summary | 2025-05-13 |
| bwa | public | The BWA read mapper. | 2025-05-13 |
| unifrac | public | Fast phylogenetic diversity calculations. | 2025-05-13 |
| starfish | public | Standardized analysis pipeline for image-based transcriptomics. | 2025-05-13 |
| cpat | public | Coding Potential Assessment Tool | 2025-05-12 |
| ectyper | public | ECtyper is a python program for serotyping E. coli genomes | 2025-05-12 |
| perl-tree-dag_node | public | An N-ary tree. | 2025-05-12 |
| methyldackel | public | A (mostly) universal methylation extractor for BS-seq experiments. Formerly named PileOMeth. | 2025-05-09 |
| illumina-interop | public | The Illumina InterOp libraries are a set of common routines used for reading and writing InterOp metric files. These metric files are binary files produced during a run providing detailed statistics about a run. In a few cases, the metric files are produced after a run during secondary analysis (index metrics) or for faster display of a subset of the original data (collapsed quality scores). | 2025-05-09 |
| mtbseq | public | Pipeline for WGS analysis of M. tuberculosis | 2025-05-07 |
| perl-crypt-openssl-rsa | public | RSA encoding and decoding, using the openSSL libraries | 2025-05-07 |
| gprofiler-official | public | Functional enrichment analysis and more via the g:Profiler toolkit | 2025-05-07 |
| flye | public | A fast and accurate de novo assembler for single molecule sequencing reads using repeat graphs. | 2025-05-07 |
| phipack | public | Simple, rapid, and statistically efficient test for recombination. | 2025-05-06 |
| bwapy | public | Bwapy provides python wrappers for bwa. | 2025-05-06 |
| regtools | public | Tools that integrate DNA-seq and RNA-seq data to help interpret mutations in a regulatory and splicing context. | 2025-05-03 |
