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    90 repositories

    • metagenomics_pooling_notebook

      Public
      Jupyter notebooks to assist with sample processing
      Jupyter Notebook
      •
      MIT License
      •16•8•45•6•Updated Nov 8, 2024Nov 8, 2024

    • microsetta-admin

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •10•0•16•3•Updated Oct 29, 2024Oct 29, 2024

    • microsetta-private-api

      Public
      A private microservice to support The Microsetta Initiative
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •19•6•60•2•Updated Oct 29, 2024Oct 29, 2024

    • mg-scripts

      Public
      Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•1•16•9•Updated Oct 21, 2024Oct 21, 2024

    • micov

      Public
      Aggregate genome coverage
      Python
      •
      Other
      •3•4•8•0•Updated Oct 20, 2024Oct 20, 2024

    • microsetta-interface

      Public
      The Microsetta participant facing user interface
      Jinja
      •
      BSD 3-Clause "New" or "Revised" License
      •17•1•45•2•Updated Oct 9, 2024Oct 9, 2024

    • q2-surpi

      Public
      A QIIME 2 plugin that connects SURPI+ results to QIIME 2 for analysis
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Oct 2, 2024Oct 2, 2024

    • q2-greengenes2

      Public
      A QIIME 2 plugin for interaction with the Greengenes2 database
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•26•5•0•Updated Oct 1, 2024Oct 1, 2024

    • gemelli

      Public
      Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
      ctfmicrobiomerpcaqiime2compositional-data-analysisrclrjoint-rpcatempted
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •18•76•29•3•Updated Oct 1, 2024Oct 1, 2024

    • calour

      Public
      exploratory and interactive microbiome analyses based on heatmaps
      bioinformaticsmicrobiomeheatmapjupyter-notebookexploratory
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •22•27•61•4•Updated Sep 29, 2024Sep 29, 2024

    • Cq-VIEW

      Public
      A qPCR-based companion to the C-VIEW (COVID-19 VIral Epidemiology Workflow) pipeline that calculates samples' viral loads.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •0•0•0•0•Updated Sep 26, 2024Sep 26, 2024

    • biom-format

      Public
      The Biological Observation Matrix (BIOM) Format Project
      Python
      •
      Other
      •95•92•25•1•Updated Aug 4, 2024Aug 4, 2024

    • empress

      Public
      A fast and scalable phylogenetic tree viewer for microbiome data analysis
      visualizationbioinformaticsmicrobiomeordinationphylogenyqiimebiplotqiime2tree-plot
      JavaScript
      •
      BSD 3-Clause "New" or "Revised" License
      •31•47•141•7•Updated Aug 4, 2024Aug 4, 2024

    • unifrac

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •16•38•17•1•Updated Jun 28, 2024Jun 28, 2024

    • improved-octo-waddle

      Public
      Balanced parentheses succinct data structure in Python
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •7•6•16•3•Updated Jun 27, 2024Jun 27, 2024

    • microsetta-processing

      Public
      Processing scripts for The Microsetta Initiative
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •1•0•1•1•Updated Jun 16, 2024Jun 16, 2024

    • qadabra

      Public
      Snakemake workflow for comparison of differential abundance ranks
      workflowbioinformaticssnakemakepipelinemetagenomicsmicrobiomedifferential-abundancemachine-learning
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•13•11•0•Updated Mar 22, 2024Mar 22, 2024

    • q2-katharoseq

      Public
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •3•1•1•3•Updated Mar 12, 2024Mar 12, 2024

    • tcga

      Public
      Microbial analysis in TCGA data
      Jupyter Notebook
      •
      BSD 3-Clause "New" or "Revised" License
      •44•89•2•6•Updated Feb 23, 2024Feb 23, 2024

    • emperor

      Public
      Emperor a tool for the analysis and visualization of large microbial ecology datasets
      bioinformaticsmicrobiomeordinationbiplotsvisualizationpythonemperor
      JavaScript
      •
      Other
      •50•52•60•2•Updated Jan 9, 2024Jan 9, 2024

    • BIRDMAn

      Public
      Bayesian Inferential Regression for Differential Microbiome Analysis
      pythonbioinformaticsregressionbayesian-inferencestanmicrobiome
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •5•22•18•1•Updated Dec 19, 2023Dec 19, 2023

    • unifrac-binaries

      Public
      C++
      •
      BSD 3-Clause "New" or "Revised" License
      •8•0•3•0•Updated Nov 14, 2023Nov 14, 2023

    • pynast

      Public archive
      Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests
      Python
      •
      Other
      •4•9•8•0•Updated Oct 30, 2023Oct 30, 2023

    • redbiom

      Public
      Sample search by metadata and features
      bioinformaticsmicrobiomeqiimebiom
      Python
      •
      Other
      •20•45•24•0•Updated Aug 31, 2023Aug 31, 2023

    • mustached-octo-ironman

      Public
      Easy dispatched compute in a Tornado environment
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •4•0•7•2•Updated Aug 14, 2023Aug 14, 2023

    • absquant

      Public
      Python
      •0•0•0•0•Updated Aug 14, 2023Aug 14, 2023

    • deblur

      Public
      Deblur is a greedy deconvolution algorithm based on known read error profiles.
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •41•92•13•12•Updated Aug 7, 2023Aug 7, 2023

    • greengenes2

      Public
      Processing support for Greengenes2
      Python
      •2•12•4•0•Updated Jul 31, 2023Jul 31, 2023

    • american-gut-web

      Public
      The website for the American Gut Project participant portal
      Python
      •
      BSD 3-Clause "New" or "Revised" License
      •24•5•49•7•Updated May 25, 2023May 25, 2023

    • q2-qemistree

      Public
      Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
      cheminformaticsphylogeneticsmetabolomicsmicrobiomefragmentation-trees
      Python
      •
      BSD 2-Clause "Simplified" License
      •16•32•23•1•Updated Apr 11, 2023Apr 11, 2023