Greg Caporaso's repositories
An-Introduction-To-Applied-Bioinformatics
Interactive lessons in bioinformatics.
biom-format
The Biological Observation Matrix (BIOM) Format Project
intro_programming
A set of IPython notebooks and learning resources for an Introduction to Programming class, focusing on Python.
built-iab
Repository for An Introduction to Applied Bioinformatics built notebooks.
cli
Command line interface for the book project (may eventually by jupyter-book)
cual-id
Code to generate pdfs of barcodes, often used for labeling sampling tubes used in microbiome research
humann
HUMAnN 3.0 is the next generation of HUMAnN 1.0 (HMP Unified Metabolic Analysis Network).
pangolin
Software package for assigning SARS-CoV-2 genome sequences to global lineages.
q2-alignment
Support for multiple sequence alignment in QIIME 2.
q2-coordinates
methods for geographic mapping of qiime2 artifact data or metadata
q2-ili
QIIME2 plugin for `ili
q2-longitudinal
QIIME2 plugin for paired sample comparisons
q2-ninja-ops
QIIME2 Plugin for NINJA-OPS
q2-phylogenomics
Phylogenomics toolkit and pipelines
q2-phylogeny
Multiple sequence alignment, phylogenetic reconstruction, and operations on phylogenetic trees.
q2-quality-control
A QIIME2 plugin for quality control of sequence and feature data
q2-shogun
A QIIME 2 plugin wrapper for the SHOGUN shallow shotgun sequencing taxonomy profiler
q2-sourmash
Qiime2 Sourmash Plugin
SHOGUN
SHallow shOtGUN profiler
sourcetracker2
SourceTracker2
the-turing-way
Host repository for The Turing Way: a how to guide for reproducible data science