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    25 repositories

    • cFMD

      Public
      Public repository for cFMD - curatedFoodMetagenomicData
      Shell
      •
      Creative Commons Attribution 4.0 International
      •4•32•0•0•Updated Feb 12, 2026Feb 12, 2026

    • preprocessing

      Public
      Raw sequence metagenomic reads pre-processing: trimming, QC, and host contamination
      pythontoolspreprocessingmetagenomesraw-reads
      Python
      •
      MIT License
      •2•14•3•1•Updated Sep 1, 2025Sep 1, 2025

    • inverse_var_weight

      Public
      Object caller for stochastically dependent and independent effect-size and meta-analysis of correlations in Python
      Python
      •0•2•0•0•Updated May 6, 2025May 6, 2025

    • CRC_staging_analysis

      Public
      Python
      •0•5•0•0•Updated Feb 2, 2025Feb 2, 2025

    • metaml

      Public
      Python
      •14•34•1•0•Updated Sep 5, 2024Sep 5, 2024

    • diet_habits_microbiome_association

      Public
      Repository with the command lines used to generate the microbiome meta-analyses and the microbiome machine learning in the vegetarian, vegan, omnivore diet comp…
      Shell
      •0•0•0•0•Updated Aug 12, 2024Aug 12, 2024

    • lefse

      Public
      Python
      •
      MIT License
      •48•87•23•2•Updated May 22, 2024May 22, 2024

    • MASTER-WP5-pipelines

      Public
      Python
      •4•4•0•1•Updated Jan 8, 2024Jan 8, 2024

    • panphlan

      Public
      PanPhlAn is a strain-level metagenomic profiling tool for identifying the gene composition of individual strains in metagenomic samples
      bioinformaticsmetagenomicsmicrobiomepangenomegene-composition
      Python
      •
      MIT License
      •6•46•11•0•Updated Oct 3, 2023Oct 3, 2023

    • metamlst

      Public
      MetaMLST is a computational tool for in-silico Multi-Locus Sequence Typing from metagenomic data.
      mlstmetagenomic-samples
      Python
      •
      MIT License
      •2•16•1•0•Updated Mar 2, 2023Mar 2, 2023

    • viromedb

      Public
      Scripts for the ViromeDB project
      Python
      •0•2•0•0•Updated Feb 13, 2023Feb 13, 2023

    • MetaRefSGB

      Public
      Python
      •0•1•1•0•Updated Feb 6, 2023Feb 6, 2023

    • hclust2

      Public
      Hclust2 is a handy tool for plotting heat-maps with several useful options to produce high quality figures that can be used in publication.
      Python
      •
      MIT License
      •4•12•10•1•Updated Jan 14, 2023Jan 14, 2023

    • viromeqc

      Public
      ViromeQC is a computational tool to benchmark and quantify non-viral contamination in VLP-enrihed viromes. ViromeQC provides an enrichment score for each virome…
      virome
      Python
      •
      MIT License
      •1•20•6•0•Updated Nov 15, 2022Nov 15, 2022

    • FMT_Meta_Machine_Learning

      Public
      R
      •
      GNU General Public License v3.0
      •0•3•0•0•Updated Aug 22, 2022Aug 22, 2022

    • MetaRefSGB_reports

      Public
      Python
      •0•1•0•0•Updated Aug 17, 2022Aug 17, 2022

    • PanPhlAn_pangenome_exporter

      Public
      Python
      •1•4•1•0•Updated Jun 3, 2022Jun 3, 2022

    • export2graphlan

      Public
      Conversion software tool for producing both annotation and tree files for GraPhlAn
      pythontoolscircular-visualization
      Python
      •
      MIT License
      •6•11•3•0•Updated Feb 2, 2022Feb 2, 2022

    • cmseq

      Public
      Set of utilities on sequences and BAM files
      Python
      •
      MIT License
      •8•27•3•0•Updated Oct 27, 2021Oct 27, 2021

    • metaclock

      Public
      A python package for assisting to reconstruct time-tree at the strain level using contemporary and ancient metagenomes.
      Python
      •
      GNU Affero General Public License v3.0
      •1•2•1•0•Updated Sep 17, 2021Sep 17, 2021

    • calculus_study_Lena_2021

      Public
      This repo contains scripts for reproducing results reported in the calculus study, Lena et al., 2021
      Python
      •0•0•0•0•Updated Jun 23, 2021Jun 23, 2021

    • Msmithii_molecular_clocking

      Public
      Code available for Marsha et al. 2021 - "Reconstruction of ancient microbial genomes from the human gut"
      Python
      •0•0•0•0•Updated Mar 17, 2021Mar 17, 2021

    • multidataset_machinelearning

      Public
      Python
      •2•1•0•0•Updated Mar 31, 2020Mar 31, 2020

    • repophlan

      Public
      Python
      •2•6•2•0•Updated Feb 17, 2020Feb 17, 2020

    • pyphlan

      Public
      Python
      •
      MIT License
      •4•5•0•0•Updated Feb 17, 2020Feb 17, 2020