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    30 repositories

    • HSPW-V3

      Public
      JavaScript
      •1•0•6•0•Updated Jul 30, 2025Jul 30, 2025

    • CAMRA

      Public
      CAMRA is a DS-I Africa research hub focused on analyzing clinical and molecular data related to antimicrobial resistance (AMR) in bacterial infections in Nigeria and Rwanda with the aim of translating genomics of AMR to sensitive, rapid diagnostics, and effective therapeutics.
      WDL
      •0•1•0•0•Updated Jul 29, 2025Jul 29, 2025

    • NSForest

      Public
      A machine learning method for the discovery of the minimum marker gene combinations for cell type identification from single-cell RNA sequencing
      machine-learningrandom-forestclusteringdecision-treessingle-cellmarker-genes
      HTML
      •
      MIT License
      •22•63•5•0•Updated Jul 25, 2025Jul 25, 2025

    • Jillion

      Public
      Jillion
      Java
      •
      GNU Lesser General Public License v2.1
      •4•2•0•0•Updated Jul 14, 2025Jul 14, 2025

    • VIGOR_DB

      Public
      VIGOR_DB
      Python
      •4•4•1•0•Updated Apr 30, 2025Apr 30, 2025

    • VIGOR4

      Public
      VIGOR4
      Java
      •
      GNU General Public License v3.0
      •13•20•4•7•Updated Apr 30, 2025Apr 30, 2025

    • LinearDisplay

      Public
      LinearDisplay.pl is a program that generates publication quality linear maps of user-defined genetic features (e.g., ORFs, promoters, transcriptional terminators, restriction enzyme recognition sites, primer-binding sites, phage attachment sites, target site duplications, assembly/contig breaks and RNA structures). It can also depict circular cl…
      Perl
      •
      GNU General Public License v3.0
      •3•9•0•0•Updated Apr 2, 2025Apr 2, 2025

    • FRmatch

      Public
      Cell type matching in single-cell RNA-sequencing data using FR-Match
      scrna-seqscrna-seq-analysiscell-type-matchingcell-typesrsingle-cell
      R
      •
      MIT License
      •2•19•1•0•Updated Mar 28, 2025Mar 28, 2025

    • DAFi-gating

      Public
      HTML
      •
      MIT License
      •3•6•0•0•Updated Jun 24, 2024Jun 24, 2024

    • celligrate

      Public
      Software suite for marker gene identification and cell type integration from single cell RNA-sequencing data
      machine-learningdata-integrationsingle-cellmarker-genesscrna-seq-analysiscell-types
      HTML
      •
      MIT License
      •0•3•1•0•Updated Jun 7, 2024Jun 7, 2024

    • PanGenomePipeline

      Public
      PanGenomePipeline
      Perl
      •
      GNU General Public License v2.0
      •9•16•7•0•Updated Apr 10, 2024Apr 10, 2024

    • PanACEA

      Public
      PanACEA is a suite of PERL scripts that allows for visualization of prokaryotic pan-chromosomes, including core and variable regions.
      Perl
      •
      GNU General Public License v2.0
      •4•7•1•0•Updated Mar 20, 2024Mar 20, 2024

    • GGRaSP

      Public
      R
      •
      GNU General Public License v2.0
      •4•7•1•0•Updated Feb 15, 2024Feb 15, 2024

    • LOCUST

      Public
      LOCUST (LOcus CUstom Sequence Typer) is a custom sequence locus typer tool for classifying microbial genomes. It provides a fully automated opportunity to customize the classification of genome-wide nucleotide variant data most relevant to biological research.
      Perl
      •
      GNU General Public License v2.0
      •2•1•1•0•Updated Jan 18, 2024Jan 18, 2024

    • veba

      Public
      A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
      Python
      •
      GNU Affero General Public License v3.0
      •10•0•0•0•Updated Oct 30, 2023Oct 30, 2023

    • OMeta-Public

      Public
      OMeta-Public
      JavaScript
      •9•8•0•4•Updated Apr 18, 2023Apr 18, 2023

    • celligrate-data

      Public
      MIT License
      •0•0•0•0•Updated Dec 20, 2022Dec 20, 2022

    • MPress

      Public
      MPress ( Microbiome power estimation with sampling and simulation)
      R
      •
      GNU General Public License v2.0
      •0•0•1•0•Updated Dec 14, 2022Dec 14, 2022

    • Flowgate_GUI

      Public
      HTML
      •0•0•3•1•Updated Oct 28, 2022Oct 28, 2022

    • pathseq2taxsummary

      Public
      Perl
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Jan 5, 2021Jan 5, 2021

    • Jillion-validation

      Public
      Bean validation for jillion
      Java
      •0•0•0•1•Updated Oct 13, 2020Oct 13, 2020

    • CDC

      Public
      CDC
      PHP
      •0•0•0•0•Updated May 9, 2019May 9, 2019

    • GUID

      Public
      GUID
      Java
      •0•1•0•0•Updated Feb 1, 2019Feb 1, 2019

    • Meta-CATS

      Public
      Metadata-driven Comparative Analysis Tool for Sequences (meta-CATS): an Automated Process for Identifying Significant Sequence Variations that Correlate with Virus Attributes
      Perl
      •1•1•0•0•Updated Nov 20, 2018Nov 20, 2018

    • HumanSubtractionDB1

      Public
      A host subtraction database for virus discovery in human cell line sequencing data
      Shell
      •0•0•0•0•Updated Jan 12, 2018Jan 12, 2018

    • HostSubtractionDB

      Public
      Shell
      •
      GNU General Public License v3.0
      •0•0•1•0•Updated Jan 11, 2018Jan 11, 2018

    • onelogin-php-sdk

      Public
      PHP
      •
      MIT License
      •20•0•0•0•Updated Jan 9, 2018Jan 9, 2018

    • SMURF

      Public
      SMURF
      0•0•0•0•Updated May 18, 2017May 18, 2017

    • mgtaxa

      Public
      A free software for taxonomic classification of metagenomic sequences with machine learning techniques
      Python
      •
      Other
      •4•0•0•0•Updated Feb 10, 2015Feb 10, 2015

    • METAREP

      Public
      METAREP: JCVI Metagenomics Reports - an open source tool for high-performance comparative metagenomics
      PHP
      •
      Other
      •10•0•0•0•Updated Mar 21, 2013Mar 21, 2013