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16s_rrna_analysis_tutorials

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

architect

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

bacarena_docker

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

brugia_metabolic_network

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

cell4d

Repository for Cell4D

cell4d_interface

deseq2_docker

Docker container for DeSeq2

detect-v2

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

eps_biofilms

HMM Models Generated from EPS Operon Prediction Project.

eukaryotic_microbiome_analysis

gut-eukaryotes-malnutrition-and-micronutrient-supplementation

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.

hitaxon

A hierarchical ensemble framework for taxonomic classification of short reads

metaanalysis-chicken-ceca-paper

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

metabolic-modeling-tools

metabolic-network-visualization

Visualizations of metabolic networks created by the Parkinson lab members

metabolic-pathways-in-microbiomes

Scripts for book chapter "Analyzing Metabolic pathways in microbiomes"

metapro

metapro_tutorial

Microbiome tutorial, running on MetaPro

metatranscriptome-workshop

Metatranscriptomics Tutorial

metawrap_docker

microbial_metafunctional_maps

microbiome_helper

An assortment of scripts to help process and automate various microbiome and metagenomic bioinformatic tools.

pathwaycompleteness

popnet

quackers

Parkinson Lab's MG pipeline prototype

running-rgi-on-scinet

Running RGI tool on MetaPro outputs on SciNet

toxonet

Repository for ToxoNet tool

tritrichomonas-murine-microbiome-interactions

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.