| Package Name | Access | Summary | Updated |
|---|---|---|---|
| imfusion | public | No Summary | 2025-09-24 |
| wgsim | public | No Summary | 2025-09-24 |
| tophat | public | A spliced read mapper for RNA-Seq. | 2025-09-24 |
| clipkit | public | Alignment trimming software for phylogenetics. | 2025-09-24 |
| phanotate | public | Phanotate gene caller for phages | 2025-09-24 |
| flash2 | public | Merge paired-end reads from fragments that are shorter than twice the read length | 2025-09-24 |
| squeakr | public | An Exact and Approximate k-mer Counting System. | 2025-09-24 |
| mira | public | MIRA is a whole genome shotgun and EST sequence assembler for Sanger, 454, Solexa (Illumina), IonTorrent data and PacBio (the later at the moment only CCS and error-corrected CLR reads). | 2025-09-24 |
| perl-sys-info-driver-osx | public | OSX driver for Sys::Info. | 2025-09-24 |
| hyphy | public | An open-source software package for comparative sequence analysis using stochastic evolutionary models. | 2025-09-24 |
| igv-reports | public | Creates self-contained html pages for visual variant review with IGV (igv.js). | 2025-09-24 |
| dbgraph | public | A graph-centric approach for metagenome-guided peptide identification in metaproteomics. | 2025-09-24 |
| miranda | public | An algorithm for finding genomic targets for microRNAs | 2025-09-24 |
| r-pathfindr | public | Enrichment analysis enables researchers to uncover mechanisms underlying a phenotype. However, conventional methods for enrichment analysis do not take into account protein-protein interaction information, resulting in incomplete conclusions. pathfindR is a tool for enrichment analysis utilizing active subnetworks. The main function identifies active subnetworks in a protein-protein interaction network using a user-provided list of genes and associated p values. It then performs enrichment analyses on the identified subnetworks, identifying enriched terms (i.e. pathways or, more broadly, gene sets) that possibly underlie the phenotype of interest. pathfindR also offers functionalities to cluster the enriched terms and identify representative terms in each cluster, to score the enriched terms per sample and to visualize analysis results. The enrichment, clustering and other methods implemented in pathfindR are described in detail in Ulgen E, Ozisik O, Sezerman OU. 2019. pathfindR: An R Package for Comprehensive Identification of Enriched Pathways in Omics Data Through Active Subnetworks. Front. Genet. <doi:10.3389/fgene.2019.00858>. | 2025-09-24 |
| ariba | public | ARIBA: Antibiotic Resistance Identification By Assembly. | 2025-09-23 |
| ra | public | Ra is short for RNA Assembler and it is a C++ implementation of an overlap-layout-consensus transcriptome assembler. | 2025-09-23 |
| vmatch | public | The Vmatch large scale sequence analysis software. | 2025-09-23 |
| links | public | Long Interval Nucleotide K-mer Scaffolder | 2025-09-23 |
| pywfa | public | A python wrapper for wavefront alignment using WFA2-lib | 2025-09-23 |
| longtr | public | Tandem repeat genotyping with long reads. | 2025-09-23 |
| metilene | public | Fast and sensitive detection of differential DNA methylation | 2025-09-23 |
| carp | public | carp - quantify the rearrangement complexity of pangenomes and their graphs. | 2025-09-23 |
| ncbitax2lin | public | NCBItax2lin | 2025-09-23 |
| humanfilt | public | WGS human-read filtering with auto-downloaded human references | 2025-09-23 |
| bin2cell | public | Join subcellular Visium HD bins into cells | 2025-09-23 |
