Greg Caporaso's repositories
2017.06.23-q2-fungal-tutorial
A quick fungal ITS analysis tutorial for QIIME 2
teaching-notebooks
A collection of IPython Notebooks that I use for teaching.
mockrobiota
A public resource for microbiome bioinformatics benchmarking.
qdr-issue14
Non-peer-reviewed analysis: Greengenes 85% OTU PyNAST alignment appears to be a suitable replacement for the Greengenes Core Set template alignment for use with PyNAST.
sketchbook
miscellaneous bioinformatics experiments
burrito-fillings
Application controllers for command line bioinformatics applications
cookiecutter-plugin-template
Cookiecutter template for initializing QIIME 2 plugin packages.
ete
ETE (Environment for Tree Exploration) is a python toolkit intended for tree analysis and visualization. It provides both a comprehensive API to manipulate and operate with trees in a programmatic way, as well as a number of command line tools to easily compare, annotate, modify or render tree images. ETE is currently developed as a research tool in the context of genomics and phylogenetics, providing several specific modules for orthology and paralogy prediction, NCBI taxonomy queries, multiple sequence alignment integration and more.
gsoc
Numfocus Google Summer of Code Materials
networkx
Official NetworkX source code repository.
pyLDAvis
Python library for interactive topic model visualization. Port of the R LDAvis package.
q2-dada2
R scripts for DADA2 QIIME2 plugin
q2-dummy-types
Dummy QIIME 2 types to serve as examples for plugin developers
q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
q2-gneiss
QIIME2 plugin for Gneiss
q2-quality-filter
Quality filtering for QIIME2
q2-sample-classifier
QIIME2 plugin for machine learning prediction of sample data.
q2-vsearch
vsearch plugin for QIIME 2
q2templates
Design template package for QIIME 2 Plugins
qiime-default-reference
Default reference data files for use with QIIME.
qiime-deploy-conf
configuration files to be used with the qiime-deploy packages
qiime-studio
A web interface for QIIME 2
qiita
Qiita - A QIIME databasing effort
qp-qiime2
Qiime 2 plugin for Qiita
scikit-bio-cookbook
Recipes for bioinformatics analyses with scikit-bio