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    17 repositories

    • snakemake-compendium

      Public
      Human Microbiome Compendium processing pipeline
      R
      •0•0•5•0•Updated Nov 4, 2024Nov 4, 2024

    • compendium

      Public
      Metadata ingest service
      Python
      •
      Apache License 2.0
      •0•0•11•0•Updated Sep 25, 2024Sep 25, 2024

    • compendium_v1

      Public
      Code associated with the first publication describing the Human Microbiome Compendium
      R
      •0•0•0•0•Updated Sep 9, 2024Sep 9, 2024

    • hominid

      Public
      Hominid: host-microbiome interaction identification
      Python
      •
      MIT License
      •3•16•2•1•Updated Jun 17, 2024Jun 17, 2024

    • milk_infant_microbiome

      Public
      Project on breast milk and infant gut microbiome
      GNU General Public License v3.0
      •1•0•0•0•Updated Jan 25, 2024Jan 25, 2024

    • compendium_website

      Public
      Website for the Human Microbiome Compendium
      TypeScript
      •1•0•1•0•Updated Jan 8, 2024Jan 8, 2024

    • snakemake-template

      Public template
      Quickstart for building out a new snakemake pipeline
      Python
      •0•0•1•0•Updated Nov 16, 2023Nov 16, 2023

    • biomehorizon

      Public
      Plot microbiome time series in parallel
      bioinformaticstimeseriesvisualizationggplot2r
      R
      •
      Other
      •2•24•5•0•Updated Nov 7, 2023Nov 7, 2023

    • biorxiv_countries

      Public
      Code repository for "International authorship and collaboration in bioRxiv preprints"
      preprintsscientific-publicationsscientific-papersscientific-publishing
      TSQL
      •
      GNU Affero General Public License v3.0
      •1•0•0•1•Updated May 22, 2023May 22, 2023

    • rxivist_web

      Public archive
      Web application for Rxivist, the site that makes it easier to find the most talked-about papers on bioRxiv.org
      Smarty
      •
      GNU Affero General Public License v3.0
      •4•11•14•0•Updated Mar 1, 2023Mar 1, 2023

    • panlingua

      Public archive
      Multilingual preprint search tool for bioRxiv
      Python
      •
      GNU Affero General Public License v3.0
      •0•1•1•0•Updated Mar 1, 2023Mar 1, 2023

    • rxivist

      Public archive
      API providing access to papers and authors scraped from biorxiv.org
      academic-publishingacademic-publicationsscientific-publicationsscientific-papersscientific-publishing
      Python
      •
      GNU Affero General Public License v3.0
      •11•60•63•0•Updated Mar 1, 2023Mar 1, 2023

    • rxivist_spider_biorxiv

      Public archive
      Web crawler that indexes preprints posted to bioRxiv.org and medRxiv.org.
      Python
      •
      GNU General Public License v3.0
      •1•1•0•0•Updated Mar 1, 2023Mar 1, 2023

    • docker_dada2

      Public
      Docker convenience image containing R and the DADA2 package (plus dependencies), used for processing amplicon data.
      docker-imagebioinformatics-containersdada2
      Dockerfile
      •2•0•1•0•Updated Jan 10, 2023Jan 10, 2023

    • host_gene_microbiome_interactions

      Public
      Analysis framework for integrating gut microbiome and host gene expression data
      R
      •12•31•3•0•Updated Apr 25, 2022Apr 25, 2022

    • Primates

      Public
      This repository contains scripts related to the publication "Interspecies variation in hominid gut microbiota controls host gene regulation."
      R
      •0•0•0•0•Updated Oct 22, 2021Oct 22, 2021

    • universal_microbiome_h2

      Public
      Files and R script for Gut microbiome heritability is near-universal but environmentally contingent
      R
      •2•0•0•0•Updated Aug 15, 2021Aug 15, 2021