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    49 repositories

    • knights-lab.github.io

      Public
      Knights Lab website via Github pages
      JavaScript
      •
      MIT License
      •0•0•0•0•Updated Oct 6, 2024Oct 6, 2024

    • MAGICstudy

      Public
      The Microbiome, Antibiotics, and Growth Infant Cohort associated analyses.
      Jupyter Notebook
      •0•0•0•0•Updated Aug 28, 2024Aug 28, 2024

    • aKronyMer

      Public
      Ultrafast genome- and dataset-scale distance matrix and phylogenetic tree creation
      C
      •1•1•0•0•Updated Jul 9, 2024Jul 9, 2024

    • BURST

      Public
      An ultrafast optimal aligner for mapping large NGS data to large genome databases.
      C
      •
      GNU Affero General Public License v3.0
      •8•57•15•0•Updated Jul 9, 2024Jul 9, 2024

    • UTree

      Public
      K-mer searching with trees
      C
      •
      GNU Affero General Public License v3.0
      •1•4•4•1•Updated Jul 9, 2024Jul 9, 2024

    • shi7

      Public
      Auto-parameterizing QC Pipeline for Illumina sequencing runs
      Python
      •
      GNU Affero General Public License v3.0
      •7•18•9•0•Updated Jul 9, 2024Jul 9, 2024

    • climate-trace-shipping

      Public
      Jupyter Notebook
      •
      MIT License
      •1•2•0•0•Updated Dec 1, 2023Dec 1, 2023

    • LMdist

      Public
      LMdist is an unsupervised algorithm for correcting oversaturated pairwise distance and dissimilarity measures. Compatible with any pairwise beta diversity measure, LMdist will uncover underlying environmental gradients and resolve arches/horseshoes in ordination.
      R
      •
      GNU Affero General Public License v3.0
      •0•5•0•0•Updated Nov 7, 2023Nov 7, 2023

    • BetaDiv

      Public
      Materials and analyses for "Microbiome beta diversity analyses and visualization." A discussion of beta diversity analysis methods, factors we must consider in each step, and how we might better use these methods in forthcoming microbiome research.
      R
      •0•0•0•0•Updated Mar 2, 2023Mar 2, 2023

    • NINJA-utils

      Public
      Reusable classes and configurations for easy Python package development.
      Python
      •
      GNU General Public License v2.0
      •1•1•0•0•Updated Aug 9, 2022Aug 9, 2022

    • DOJO

      Public
      Python
      •
      GNU General Public License v2.0
      •1•1•1•0•Updated Aug 8, 2022Aug 8, 2022

    • ermin-standards

      Public
      Emissions Report Minimum INformation (ERMIN) Standards
      Python
      •
      MIT License
      •1•2•8•0•Updated Apr 28, 2022Apr 28, 2022

    • SHOGUN

      Public
      SHallow shOtGUN profiler
      Python
      •
      GNU Affero General Public License v3.0
      •19•54•18•1•Updated Mar 4, 2022Mar 4, 2022

    • MLRepo

      Public
      R
      •
      MIT License
      •13•34•0•0•Updated Jan 13, 2022Jan 13, 2022

    • foodworks

      Public
      Experimenting with Bayesian Networks for predicting day-to-day microbiome fluctuations
      Jupyter Notebook
      •
      MIT License
      •0•0•0•0•Updated Jan 9, 2022Jan 9, 2022

    • helix

      Public
      Short scripts for use within the knights-lab
      Python
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Dec 28, 2021Dec 28, 2021

    • type_1

      Public
      Jupyter Notebook
      •
      GNU Affero General Public License v3.0
      •0•0•0•0•Updated Oct 28, 2021Oct 28, 2021

    • conda-recipes

      Public
      Conda recipes for the knights lab
      Python
      •
      GNU General Public License v2.0
      •1•1•1•0•Updated Jul 3, 2021Jul 3, 2021

    • IMP_analyses

      Public
      immigrant microbiome project related analyses
      R
      •4•4•0•0•Updated May 8, 2021May 8, 2021

    • analysis_italy

      Public
      Jupyter Notebook
      •0•0•0•0•Updated Feb 16, 2021Feb 16, 2021

    • analysis_tree

      Public
      Python
      •1•1•0•0•Updated Feb 28, 2020Feb 28, 2020

    • Food_Tree

      Public
      USDA Nutrition codes Tree
      R
      •
      GNU General Public License v3.0
      •7•10•0•0•Updated Feb 13, 2020Feb 13, 2020

    • analysis_SHOGUN

      Public
      Analysis scripts and code for reproducing the analysis for the SHOGUN paper
      Jupyter Notebook
      •
      MIT License
      •1•1•13•0•Updated Feb 10, 2020Feb 10, 2020

    • dietstudy_analyses

      Public
      R
      •9•11•0•0•Updated Jun 12, 2019Jun 12, 2019

    • douc_gut_sites

      Public
      Microbiome of red-shanked douc gut sites
      R
      •1•0•0•0•Updated Mar 14, 2019Mar 14, 2019

    • dietstudy

      Public
      Diet Study
      JavaScript
      •0•0•0•0•Updated Jan 31, 2019Jan 31, 2019

    • megaperm

      Public
      Two-group, two-timepoint non-parametric permutation-based significance testing allowing for uneven repeated sampling (whew!)
      R
      •0•0•1•0•Updated Jul 10, 2018Jul 10, 2018

    • kafan

      Public
      Lossless data compression codec specialized for sequence data
      C
      •
      GNU Affero General Public License v3.0
      •0•1•0•0•Updated Jul 10, 2018Jul 10, 2018

    • IMP-Open-Ref

      Public
      Open Ref BURST with IMP data
      R
      •0•0•0•0•Updated Feb 20, 2018Feb 20, 2018

    • q2-ninja-ops

      Public
      QIIME2 Plugin for NINJA-OPS
      Python
      •
      ISC License
      •3•1•0•1•Updated Feb 7, 2018Feb 7, 2018