18 open source projects by biocore

Code repository of the Earth Microbiome Project.

SortMeRNA: next-generation sequence filtering and alignment tool

American Gut open-access data and IPython notebooks

Deblur is a greedy deconvolution algorithm based on known read error profiles.

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

scikit-bio is an open-source, BSD-licensed, Python package providing data structures, algorithms, and educational resources for bioinformatics.

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

Sample search by metadata and features

Confirming specific taxonomic groups within your samples.

Vanilla regression methods for microbiome differential abundance analysis

exploratory and interactive microbiome analyses based on heatmaps

Microbial analysis in TCGA data

annotation pipeline for microbial genomes and metagenomes

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

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

compositional data analysis toolbox

Neural networks for microbe-metabolite interaction analysis

A fast and scalable phylogenetic tree viewer for microbiome data analysis