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@cmmr Alkek Center for Metagenomics and Microbiome Research

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    18 repositories

    • nextflow

      Public
      16S and WGS Pipelines
      Shell
      •0•0•0•0•Updated Aug 20, 2026Aug 20, 2026

    • h5lite

      Public
      Read/write HDF5 datasets and attributes from R
      R
      •
      Other
      •0•3•0•0•Updated Jul 22, 2026Jul 22, 2026

    • hdf5lib

      Public
      HDF5 C Library for R
      C
      •
      Other
      •0•1•0•0•Updated Jul 22, 2026Jul 22, 2026

    • EsViritu

      Public
      Read mapping pipeline for detection and measurement of virus pathogens from metagenomic or clinical data
      bioinformaticsngsmetagenomics
      bioinformaticsngsmetagenomicsvirusesviromepathogens
      Python
      •
      MIT License
      •10•54•2•0•Updated Jul 21, 2026Jul 21, 2026

    • ecodive

      Public
      Parallel and Memory-Efficient R Package for Ecological Diversity Analysis
      R
      •
      Other
      •0•8•0•0•Updated Jun 4, 2026Jun 4, 2026

    • rbiom

      Public
      An R Package for Integrated Analysis and Visualization of Microbiome Data
      R
      •
      Other
      •1•19•3•0•Updated May 7, 2026May 7, 2026

    • cmmr.github.io

      Public
      CMMR Developer News
      HTML
      •0•0•0•0•Updated Mar 7, 2026Mar 7, 2026

    • fillpattern

      Public
      Patterned Fills for R's ggplot2 and grid Graphics
      R
      •
      Other
      •0•13•0•0•Updated Feb 13, 2026Feb 13, 2026

    • Marker-MAGu

      Public
      Trans-Kingdom Marker Gene Pipeline for Taxonomic Profiling of Human Metagenomes
      Python
      •
      MIT License
      •1•23•4•0•Updated Nov 24, 2025Nov 24, 2025

    • interprocess

      Public
      Mutexes, Semaphores, and Message Queues for R
      R
      •
      Other
      •0•12•0•0•Updated Aug 7, 2025Aug 7, 2025

    • jobqueue

      Public
      Queue and Run Asynchronous Interruptible R Tasks on Background Processes
      R
      •
      Other
      •0•2•0•0•Updated Aug 7, 2025Aug 7, 2025

    • webqueue

      Public
      HTTP Server Using Multiple CPU Cores
      R
      •
      Other
      •0•2•1•0•Updated May 24, 2025May 24, 2025

    • semaphore

      Public
      Shared Memory Atomic Operations in R
      R
      •
      Other
      •0•2•0•0•Updated May 23, 2025May 23, 2025

    • TX_wastewater_virome

      Public
      HTML
      •0•7•1•0•Updated Mar 7, 2024Mar 7, 2024

    • virmap

      Public
      Perl
      •
      GNU Affero General Public License v3.0
      •14•25•17•0•Updated Feb 2, 2021Feb 2, 2021

    • covid

      Public archive
      COVID-19 Dashboard coded in Shiny R
      R
      •
      GNU Affero General Public License v3.0
      •1•0•0•0•Updated Jun 26, 2020Jun 26, 2020

    • puma-deprecated

      Public archive
      Code for the unreleased/unpublished PUMA pipeline.
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jan 7, 2020Jan 7, 2020

    • NashMicrobiome2017

      Public archive
      Pipeline for Fungal Community Analysis
      Perl
      •
      GNU General Public License v3.0
      •0•0•0•0•Updated Jul 19, 2017Jul 19, 2017
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