Skip to content

@knights-lab knights-lab

All

    Repositories list

    50 repositories

    • UTree

      Public
      K-mer searching with trees
      C
      •
      GNU Affero General Public License v3.0
      •3•5•4•1•Updated Mar 26, 2026Mar 26, 2026

    • MAGEnTa

      Public
      Pipeline for metagenomic source tracking
      0•0•0•0•Updated Jul 11, 2025Jul 11, 2025

    • 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•60•15•0•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•3•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 measu…
      R
      •
      GNU Affero General Public License v3.0
      •0•7•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 …
      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
      •17•52•19•1•Updated Mar 4, 2022Mar 4, 2022

    • MLRepo

      Public
      R
      •
      MIT License
      •14•39•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•11•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
      •8•12•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
    ProTip! When viewing an organization's repositories, you can use the props. filter to filter by custom property.