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ampliseq

16S rRNA amplicon sequencing analysis workflow using QIIME2

amr-nextflow

A Nextflow-based set of scripts for running the MEG Antimicrobial Resistance AmrPlusPlus pipeline

amr_one_health_2021

One Health Summer Institute's Introduction to Bioinformatics workshop. Session on Bioinformatics for AMR Research.

amrplusplus-shiny

Statistical analyses for outputs of the AMR++ analytic pipeline

amrplusplus_helper_scripts

amrplusplus_v2

MEGARes and AmrPlusPlus - A comprehensive database of antimicrobial resistance genes and user-friendly pipeline for analysis of high-throughput sequencing data

bacass

Simple bacterial assembly and annotation pipeline.

badas_nextflow_tutorial

Nextflow tutorial for the BADAS series at NYU Center for Genomics and Systems Biology

bcrc_comparative_study

:cow: :pill: :cow2: :poop: BCRC comparative metagenomics study

beebiome-data-portal

A resource for scientists and the general public on bee-associated microbes/viruses and their impact on bee health

beebiome-taxonomy-scripts

bioconda-recipes

Conda recipes for the bioconda channel.

boa-wgs

A Snakemake workflow for the analysis of bacterial WGS data

bohra

A pipeline for bioinformatics analysis of bacterial genomes

bothie

camisim

CAMISIM: Simulating metagenomes and microbial communities

card-krakendb

Scripts for creating a Kraken database from the Comprehensive Antibiotic Resistance Database

chord-diagram-storytelling

Using storytelling to explain a Chord Diagram about phone brand switching behaviour

coda_microbiome_tutorial

Workshop for NGS'18 conference, Barcelona 2018

commandlinetutorial

Guide to useful commands for the terminal

common-workflow-language

Repository for CWL Specifications. Use https://www.biostars.org/t/cwl/ for support.

cookiecutter-conda-python

A cookiecutter template for conda packages using Python

cookiecutter-snakemake-workflow

A cookiecutter template for Snakemake workflows

cv

My YAML cv and resume.

dada2_drake_workflow

dl-interpretability-compbio

drax

A pipeline for Detecting Resistome Associated taXa

edirectcookbook

enterocomp

Analysis of Enterococcus AST profiles and marker genes

fieldimager-workshop-11

Workshop presented for NDSU Breeding Pipeline Database Managers. In this course, I went through the basic steps of the FIELDimageR pipeline showing how to evaluate and apply remote sensing data in plant breeding.