Ben Kaehler's repositories
readytowear
Ready-made Taxonomic Weights Repository
q2-makarsa
A QIIME 2 plugin to generate and visualise microbial networks.
q2-clawback
This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.
mm-project-2020
Examples and stubs to form the basis of the ZPEM2311 Mathematical Modelling Major Project for 2020.
why-bother
Some ideas for non-stationary, rooted, strand-symmetric phylogenetic tree discovery.
ANCOM
R scripts for Analysis of Composition of Microbiomes (ANCOM).
BenKaehler.github.io
Ben's Website
cogent3
Comparative Genomics Toolkit 3
docs
Source repository for https://docs.qiime2.org
game17
Run game17
mockrobiota-utilities
Utility scripts for use with mockrobiota
q2-feature-classifier
QIIME 2 plugin supporting taxonomic classification
q2-feature-table
QIIME 2 plugin supporting operations on feature tables.
q2-ipcress
QIIME 2 wrapper for ipcress, an in-silico PCR experiment simulation system
q2-sample-classifier
QIIME 2 plugin for machine learning prediction of sample data.
redbiom
Sample search by metadata and features
RESCRIPt
REference Sequence annotation and CuRatIon Pipeline
scikit-learn
scikit-learn: machine learning in Python
short-read-tax-assignment
A repository for storing code and data related to a systematic comparison of short read taxonomy assignment tools
silva-trees
Some SILVA trees
SpiecEasi
Sparse InversE Covariance estimation for Ecological Association and Statistical Inference
tax-credit-code
Microbiome benchmarking code and jupyter notebooks from the tax-credit project
tax-credit-data
raw data from tax-credit project