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    71 repositories

    • samovar

      Public
      Development of a algorithms packages for generating model metagenomes with specified properties
      Jupyter Notebook
      •0•5•2•0•Updated Nov 23, 2024Nov 23, 2024

    • GADMA

      Public
      Genetic Algorithm for Demographic Model Analysis
      Python
      •
      Other
      •14•47•8•0•Updated Nov 6, 2024Nov 6, 2024

    • fgsea

      Public
      Fast Gene Set Enrichment Analysis
      R
      •
      Other
      •68•379•14•0•Updated Oct 8, 2024Oct 8, 2024

    • phantasus

      Public
      Visual exploratory analysis of gene expression data
      HTML
      •
      Other
      •15•43•23•0•Updated Oct 8, 2024Oct 8, 2024

    • parallel-rearrangements

      Public
      parallel rearrangements caller
      Python
      •
      MIT License
      •2•4•2•0•Updated Oct 6, 2024Oct 6, 2024

    • phantasus.js

      Public
      JavaScript matrix visualization and analysis
      JavaScript
      •22•2•0•2•Updated Sep 16, 2024Sep 16, 2024

    • mwcsr

      Public
      An R package for solving maximum-weight connected subrgaph problem and it's variants
      rcplex
      C++
      •
      Other
      •3•7•0•0•Updated Sep 9, 2024Sep 9, 2024

    • metafast

      Public
      Fast metagenome analysis toolkit
      Java
      •
      MIT License
      •10•26•0•1•Updated Sep 3, 2024Sep 3, 2024

    • phantasusLite

      Public
      R
      •
      Other
      •2•7•0•0•Updated Aug 28, 2024Aug 28, 2024

    • phantasus-doc

      Public
      Phantasus documentation
      Ruby
      •0•0•0•0•Updated Jul 18, 2024Jul 18, 2024

    • HiCT

      Public
      Combines all HiCT-related repositories as submodules
      Dockerfile
      •
      MIT License
      •0•2•1•0•Updated Jun 26, 2024Jun 26, 2024

    • HiCT_Library

      Public
      Library for interaction with Hi-C contact maps in HDF5 format
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • HiCT_JVM

      Public
      Interactive visualizer ad manual scaffolder of Hi-C contact maps. All-in-one Java-based implementation.
      visualizationjavagenomegradleopenlayershdf5hi-citmoscaffoldinghdf5-format
      Java
      •
      MIT License
      •0•1•7•0•Updated Jun 26, 2024Jun 26, 2024

    • HiCT_Server

      Public
      Python
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • HiCT_Utils

      Public
      Utilities for interaction with HiCT library and data format.
      Python
      •
      MIT License
      •0•0•1•0•Updated Jun 26, 2024Jun 26, 2024

    • HiCT_WebUI

      Public
      TypeScript
      •
      MIT License
      •0•0•0•0•Updated Jun 26, 2024Jun 26, 2024

    • scNavigator

      Public
      Single Cell Navigator
      JavaScript
      •2•5•0•2•Updated May 15, 2024May 15, 2024

    • BandageNG

      Public
      a Bioinformatics Application for Navigating De novo Assembly Graphs Easily
      C++
      •
      GNU General Public License v3.0
      •98•0•0•0•Updated May 12, 2024May 12, 2024

    • gatom

      Public
      Finding an Active Metabolic Module in Atom Transition Network
      R
      •
      Other
      •4•5•1•0•Updated Apr 30, 2024Apr 30, 2024

    • metafx

      Public
      MetaFX – library for feature extraction from whole-genome metagenome sequencing data
      bioinformaticsmetagenomicsfeature-extraction
      Shell
      •
      MIT License
      •1•10•0•0•Updated Apr 16, 2024Apr 16, 2024

    • phantasus-preimage

      Public
      Opencpu + Bioconductor + devtools docker image to speed up phantasus builds
      Dockerfile
      •0•0•0•0•Updated Mar 29, 2024Mar 29, 2024

    • GAMclust

      Public
      GAM-clustering: Metabolic Modules Derivig From RNAseq Data
      HTML
      •
      Other
      •0•2•1•0•Updated Mar 19, 2024Mar 19, 2024

    • metacherchant

      Public
      bioinformaticsmetagenomics
      Java
      •
      MIT License
      •9•18•2•2•Updated Jan 16, 2024Jan 16, 2024

    • evoguess-ai

      Public
      Component for finding decomposition sets and estimating hardness of SAT instances.
      Python
      •
      MIT License
      •0•4•0•0•Updated Jan 15, 2024Jan 15, 2024

    • true-dist-infer

      Public
      HTML
      •0•1•0•0•Updated Sep 15, 2023Sep 15, 2023

    • GScour

      Public
      Genome-wide detection of positive selection
      positive-selectionbioinformatics
      Python
      •0•9•0•0•Updated Jun 6, 2023Jun 6, 2023

    • evoguess

      Public
      Component EvoGuess v2.1 for finding decomposition sets and estimating hardness of SAT instances.
      Python
      •
      MIT License
      •1•2•0•0•Updated Jun 4, 2023Jun 4, 2023

    • metafx_old

      Public archive
      Jupyter Notebook
      •
      MIT License
      •0•1•0•0•Updated May 23, 2023May 23, 2023

    • dadi_adjoint_state

      Public
      The adjoint-state method for demographic inference
      Python
      •0•0•0•0•Updated May 21, 2023May 21, 2023

    • virgo-solver

      Public
      Solver for SGMWCS and GMWCS problems
      Java
      •
      Other
      •1•3•0•0•Updated May 16, 2023May 16, 2023