Michael Shaffer's repositories
fast_sparCC
A fast command line interface to find correlations in biom tables with sparCC.
dada2_qiime1
Using DADA2 for to generate necessary files for QIIME 1 analyses.
q2-network
A QIIME2 plugin for basic network analyses and generating correlation networks from traditional statistics.
SCNIC_QIIME2_workshop_SD_2018
All analyses to generate data and figures for the SCNIC talk at the 2018 QIIME2 Developers Workshop in San Diego
bioconda-recipes
Conda recipes for the bioconda channel.
bioinfo_tools
Set of basic tools for bioinformatics
biom-format
The Biological Observation Matrix (BIOM) Format Project
michael_shafferContigFilter
KBase tutorial app
microbiome_metab
Scripts for analyzing metabolism in microbiomes. Focused on the use and extension of QIIME and PICRUSt methods.
micrometab_kb
A simple website for exploration of metabolism of bacteria based on 16S sequences and the KEGG database.
spacer-seeker
A fast fuzzy string matching program for the identification and analysis of spacer origin using CRISPR and viral sequences.
VirSorter
KBase integration of VirSorter