Repositories list

• HSPW-V3

  Public
  JavaScript

  •1•0•5•0•Updated Jan 15, 2025Jan 15, 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 Jan 6, 2025Jan 6, 2025

• FRmatch

  Public
  Cell type matching in single-cell RNA-sequencing data using FR-Match

  scrna-seqscrna-seq-analysiscell-type-matching+ 3cell-typesrsingle-cell

  R

  •

  MIT License

  •2•19•0•0•Updated Oct 9, 2024Oct 9, 2024

• 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-forestclustering+ 3decision-treessingle-cellmarker-genes

  HTML

  •

  MIT License

  •20•57•4•2•Updated Oct 7, 2024Oct 7, 2024

• Jillion

  Public
  Jillion

  Java

  •

  GNU Lesser General Public License v2.1

  •4•2•0•0•Updated Aug 8, 2024Aug 8, 2024

• DAFi-gating

  Public
  HTML

  •

  MIT License

  •2•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-cell+ 3marker-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•15•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

• VIGOR4

  Public
  VIGOR4

  Java

  •

  GNU General Public License v3.0

  •11•18•4•7•Updated Jun 14, 2023Jun 14, 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

• VIGOR_DB

  Public
  VIGOR_DB

  Python

  •3•3•1•0•Updated Dec 2, 2022Dec 2, 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

• 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•6•0•0•Updated Sep 11, 2019Sep 11, 2019

• 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

  •11•0•0•0•Updated Mar 21, 2013Mar 21, 2013