| Package Name | Access | Summary | Updated |
|---|---|---|---|
| phynteny_transformer | public | Phynteny: Synteny-based prediction of bacteriophage genes. | 2025-06-05 |
| perl-file-find-rule | public | Alternative interface to File::Find. | 2025-06-05 |
| hicberg | public | Statistical profiling based tool for contact data (Hi-C, ChIA-PET, Capture-C, etc.) and genomics data reconstruction | 2025-06-05 |
| pacini_typing | public | YAML-based bacterial genotyping application | 2025-06-05 |
| virulencefinder | public | VirulenceFinder identifies virulence genes in total or partial sequenced isolates of bacteria | 2025-06-05 |
| pasta | public | An implementation of the PASTA (Practical Alignment using Sate and TrAnsitivity) algorithm. | 2025-06-05 |
| giatools | public | Tools required for Galaxy Image Analysis | 2025-06-05 |
| metaphlan | public | Metagenomic Phylogenetic Analysis. | 2025-06-04 |
| pretextsnapshot | public | Commandline image generator for Pretext Hi-C genome contact maps. | 2025-06-04 |
| bowtie2 | public | A fast and sensitive gapped read aligner. | 2025-06-03 |
| r-tmae | public | Tests and visualizations for mono-allelicly expressed variants. | 2025-06-03 |
| bcftools-liftover-plugin | public | Tools to work with GWAS-VCF summary statistics files (liftover plugin only) | 2025-06-03 |
| k8 | public | Lightweight JavaScript shell based on Google's V8 JavaScript engine | 2025-06-03 |
| quota_anchor | public | Strand and WGD aware syntenic gene identification | 2025-06-03 |
| iced | public | The python module iced implements the ICE normalization of hic data. | 2025-06-03 |
| rustybam | public | Mitchell Vollger's bioinformatics rust utilities. | 2025-06-03 |
| vqbg | public | De Novo Reconstruction of Viral Quasispecies from Bubble Graph | 2025-06-03 |
| rucs | public | RUCS is a bioinformatics tool developed to ease the task of designing new primers. | 2025-06-03 |
| riboloco | public | Riboseq analysis. | 2025-06-03 |
| transit | public | TRANSIT | 2025-06-02 |
| uniprot-id-mapper | public | A Python wrapper for the UniProt Mapping RESTful API. | 2025-06-02 |
| r-tinc | public | TINC is a package that implements algorithms to determine the contamination of a bulk sequencing sample in the context of cancer studies (matched tumour/ normal). The contamination estimated by TINC can be either due to normal cells sampled in the tumour biopsy or to tumour cells in the normal biopsy. The former case is traditionally called purity, or cellularity, and a number of tools exist to estimate it. The latter case is less common, and that is the main reason TINC has been developed. For this reason, the package takes name TINC, Tumour-in-Normal contamination. TINC is part of the evoverse, a package that gathers multiple R packages to implement Cancer Evolution analyses. | 2025-06-02 |
| longtrack | public | Track FMT strains using long-read metagenomic assemblies. | 2025-06-02 |
| freebayes | public | Bayesian haplotype-based polymorphism discovery and genotyping. | 2025-06-02 |
| diatracer | public | A diaPASEF spectrum-centric analysis tool | 2025-06-02 |
