Repositories list

• MetaPro

  Public
  Python

  •

  GNU General Public License v3.0

  •4•19•4•0•Updated Jan 15, 2025Jan 15, 2025

• seq_cleaner

  Public
  Repo for a simple sequence cleaner. Removes host data, and filters for low-quality reads

  Python

  •0•0•0•0•Updated Jan 10, 2025Jan 10, 2025

• quackers

  Public
  Parkinson Lab's MG pipeline prototype

  Python

  •0•1•2•0•Updated Nov 22, 2024Nov 22, 2024

• bacarena_docker

  Public
  stash for bacarena docker build/install for version-lock/distribution among lab.

  Dockerfile

  •0•0•0•0•Updated Nov 4, 2024Nov 4, 2024

• 16S_MGX_Workshops

  Public
  1•0•0•0•Updated Oct 26, 2024Oct 26, 2024

• Chicken_microbiome

  Public
  Repository for Chicken Microbiome project

  R

  •0•0•0•0•Updated Oct 16, 2024Oct 16, 2024

• HiTaxon

  Public
  A hierarchical ensemble framework for taxonomic classification of short reads

  Python

  •0•1•0•0•Updated May 20, 2024May 20, 2024

• MetaPro_tutorial

  Public
  Microbiome tutorial, running on MetaPro

  2•2•0•0•Updated May 6, 2024May 6, 2024

• PathwayCompleteness

  Public
  Jupyter Notebook

  •0•0•0•0•Updated Apr 26, 2024Apr 26, 2024

• cell4d

  Public
  Repository for Cell4D

  C++

  •

  Other

  •0•0•0•0•Updated Feb 13, 2024Feb 13, 2024

• metawrap_docker

  Public
  Dockerfile

  •0•0•0•0•Updated Jan 10, 2024Jan 10, 2024

• DeSeq2_docker

  Public
  Docker container for DeSeq2

  Dockerfile

  •0•0•0•0•Updated Jan 2, 2024Jan 2, 2024

• Running-RGI-on-SciNet

  Public
  Running RGI tool on MetaPro outputs on SciNet

  0•0•0•0•Updated Nov 8, 2023Nov 8, 2023

• Metatranscriptome-Workshop

  Public
  Metatranscriptomics Tutorial

  23•60•11•0•Updated Jul 3, 2023Jul 3, 2023

• Architect

  Public
  Pipeline for automatic metabolic model reconstruction using an ensemble method for enzyme annotation

  Python

  •

  GNU General Public License v3.0

  •0•6•3•0•Updated Jun 5, 2023Jun 5, 2023

• eps_biofilms

  Public
  HMM Models Generated from EPS Operon Prediction Project.

  bacterial-operonshmms

  Perl

  •0•1•0•0•Updated Mar 7, 2023Mar 7, 2023

• metabolic-modeling-tools

  Public
  1•0•0•1•Updated Mar 2, 2023Mar 2, 2023

• ToxoNet

  Public
  Repository for ToxoNet tool

  C

  •0•1•0•0•Updated Dec 1, 2022Dec 1, 2022

• 16S_rRNA_analysis_tutorials

  Public
  The tutorials under this repository will take you through workflows for processing and analyzing 16S rRNA data.

  0•0•0•0•Updated Nov 11, 2022Nov 11, 2022

• DETECT-v2

  Public
  Version 2 of the Density Estimation Tool for Enzyme ClassificaTion: scripts for enzyme annotation and pipeline for making the DETECT database

  Python

  •

  Other

  •3•4•0•0•Updated Jun 30, 2022Jun 30, 2022

• Tritrichomonas-murine-microbiome-interactions

  Public
  A project interrogating the activities of murine gut protozoan Tritrichomonas, and its impact on the bacterial communities in healthy and IgA-deficient hosts. This study includes a protozoan draft genome assembly, single cell RNA-Seq data, and 16S bacterial and metatranscriptomics sequencing over the first month of colonization.

  MIT License

  •1•0•0•0•Updated Apr 11, 2022Apr 11, 2022

• gut-eukaryotes-malnutrition-and-micronutrient-supplementation

  Public
  Collection of codes used in the analysis of 16S and 18S rRNA sequencing surveys, which were conducted on stool DNA from healthy and malnourished children from Pakistan.

  R

  •

  GNU General Public License v3.0

  •1•0•0•0•Updated Oct 27, 2021Oct 27, 2021

• Eukaryotic_microbiome_analysis

  Public
  R

  •

  GNU General Public License v3.0

  •5•0•0•0•Updated Mar 31, 2021Mar 31, 2021

• cell4d_interface

  Public
  0•0•0•0•Updated Nov 11, 2020Nov 11, 2020

• PopNet

  Public
  Python

  •2•3•0•0•Updated Sep 21, 2020Sep 21, 2020

• Brugia_metabolic_network

  Public
  Files pertaining to our paper on the genome-scale metabolic network reconstruction for Brugia malayi.

  GNU General Public License v2.0

  •2•0•0•0•Updated Jul 23, 2020Jul 23, 2020

• microbial_metafunctional_maps

  Public
  JavaScript

  •0•0•0•0•Updated Jun 3, 2020Jun 3, 2020

• Metabolic-network-visualization

  Public
  Visualizations of metabolic networks created by the Parkinson lab members

  1•0•0•0•Updated Dec 12, 2018Dec 12, 2018

• metaanalysis-chicken-ceca-paper

  Public
  scripts and tables used to generate figures in chicken cecal microbiome metanalysis paper

  Python

  •0•0•0•0•Updated Oct 10, 2018Oct 10, 2018

• Metabolic-pathways-in-microbiomes

  Public
  Scripts for book chapter "Analyzing Metabolic pathways in microbiomes"

  R

  •2•3•0•0•Updated Jul 17, 2018Jul 17, 2018