Name: Greg Caporaso
Type: User
Company: @qiime2
Bio: Program Manager and PI (@qiime2);
Professor of Biology and CS (@caporaso-lab, @applied-bioinformatics, @4cscc).
Location: Flagstaff, Arizona, USA
Blog: cap-lab.bio
Greg Caporaso's Projects
Test of creating a Software Carpentry Workshop Website for the Teaching11 course
A quick fungal ITS analysis tutorial for QIIME 2
Interactive lessons in bioinformatics.
Template for Software Carpentry bootcamp site repository.
The Biological Observation Matrix (BIOM) Format Project
Repository for An Introduction to Applied Bioinformatics built notebooks.
Application controllers for command line bioinformatics applications
JupyterBook for QIIME 2 FAES January 2022 workshop
Command line interface for the book project (may eventually by jupyter-book)
Automated testing system for development versions of QIIME, PyCogent, biom-format, and more.
Cookiecutter template for initializing QIIME 2 plugin packages.
Code to generate pdfs of barcodes, often used for labeling sampling tubes used in microbiome research
Accurate sample inference from amplicon data with single nucleotide resolution
A Python library for phylogenetic scripting, simulation, data processing and manipulation.
Developer documentation for QIIME 2
Developing with QIIME 2
A systematic approach to creating better documentation.
Source repository for https://docs.qiime2.org
Emperor a tool for the analysis and visualization of large microbial ecology datasets
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.
An attempt to ease the creation of QIIME 2 manifest files