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Package Name Access Summary Updated
snakemake-minimal public A popular workflow management system aiming at full in-silico reproducibility. 2025-09-24
snakemake public A popular workflow management system aiming at full in-silico reproducibility. 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
cenmap public A centromere mapping and annotation pipeline for T2T human and primate genome assemblies implemented in Snakemake. 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
gather public Assembly of heavy and light chain BCRs using De Bruijn graphs. 2025-09-23
novoloci public Haplotype-aware assembler for complex regions and small genomes (ONT/HiFi). 2025-09-23
switchtfi public Implementation of the SwitchTFI method as presented in: https://doi.org/10.1101/2025.01.20.633856 2025-09-23
cagecleaner public Genomic redundancy removal tool for cblaster hit sets. 2025-09-23
ipcr public In-silico PCR with mismatch thresholds and pretty alignment output. 2025-09-23
gap2seq public Gap2Seq is a tool for filling gaps between contigs in genome assemblies. 2025-09-23

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