benkaehler Goto Github PK

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

gapped

ancestral state reconstruction

mm-labs

ZPEM2311 Mathematical Modelling Lab Notebooks

mm-major-project-2020

mm-project-2020

Examples and stubs to form the basis of the ZPEM2311 Mathematical Modelling Major Project for 2020.

mockrobiota

A public resource for microbiome bioinformatics benchmarking using artificially constructed (i.e., mock) communities.

mockrobiota-utilities

Utility scripts for use with mockrobiota

paycheck

tAxonomY Classification Expected Composition

pretrained-feature-classifiers

pycogent

PyCogent: Official repository for software and unit tests

pystruct

Simple structured learning framework for python

q2-clawback

This is a QIIME 2 plugin. For details on QIIME 2, see https://qiime2.org.

q2-extra-classifier

q2-feature-classifier

QIIME 2 plugin supporting taxonomic classification

q2-feature-classifier-tuning

Grid search notebooks for the classifiers in q2-feature-classifier

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-makarsa

A QIIME 2 plugin to generate and visualise microbial networks.

q2-sample-classifier

QIIME 2 plugin for machine learning prediction of sample data.

q2-types

Definitions of common QIIME 2 types.

qiime2

Official repository for the QIIME 2 framework

readytowear

Ready-made Taxonomic Weights Repository

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