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ahdilmore

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amplicon-gpt

modifications to kalen's amplicon GPT to adapt for classifier use

beam_multiomics

Code for analyses for BEAM manuscript

deicode

Robust Aitchison PCA from sparse count data

emperor

Emperor a tool for the analysis and visualization of large microbial ecology datasets

empress

A fast and scalable phylogenetic tree viewer for microbiome data analysis

gemelli

Gemelli is a toolbox for running both Robust Aitchison PCA (RPCA) and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.

genomicuf

Constructs per-gene phylogenetic trees from [meta]genomic sequencing data enabling calculation of UniFrac distance across multiple gene histories.

mars_birdman

Outlines for running birdman

metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing

multiomics

resources from my multi-omics code review presentation :)

pths_notebooks

Jupyter notebooks and data for PTHS manuscript

q2-dada2

QIIME 2 plugin wrapping DADA2

q2-deblur

q2-diversity

q2-emperor

q2-feature-table

QIIME 2 plugin supporting operations on feature tables.

q2-qemistree

Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".

qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

qiime2r

Import qiime2 artifacts to R

qurro

Visualize differentially ranked features (taxa, metabolites, ...) and their log-ratios across samples

songbird

Vanilla regression methods for microbiome differential abundance analysis

tulsa1000_microbiome

Code to generate figures for Tulsa manusript