Pinned Repositories
American-Gut
American Gut open-access data and IPython notebooks
biom-format
The Biological Observation Matrix (BIOM) Format Project
deblur
Deblur is a greedy deconvolution algorithm based on known read error profiles.
emp
Code repository of the Earth Microbiome Project.
gemelli
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
gneiss
compositional data analysis toolbox
mmvec
Neural networks for microbe-metabolite interaction analysis
qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
songbird
Vanilla regression methods for microbiome differential abundance analysis
tcga
Microbial analysis in TCGA data
biocore's Repositories
biocore/biom-format
The Biological Observation Matrix (BIOM) Format Project
biocore/deblur
Deblur is a greedy deconvolution algorithm based on known read error profiles.
biocore/tcga
Microbial analysis in TCGA data
biocore/gemelli
Gemelli is a tool box for running Robust Aitchison PCA (RPCA), Joint Robust Aitchison PCA (Joint-RPCA), TEMPoral TEnsor Decomposition (TEMPTED), and Compositional Tensor Factorization (CTF) on sparse compositional omics datasets.
biocore/emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets
biocore/empress
A fast and scalable phylogenetic tree viewer for microbiome data analysis
biocore/redbiom
Sample search by metadata and features
biocore/unifrac
biocore/q2-qemistree
Hierarchical orderings for mass spectrometry data. Canonically pronounced "chemis-tree".
biocore/calour
exploratory and interactive microbiome analyses based on heatmaps
biocore/q2-greengenes2
A QIIME 2 plugin for interaction with the Greengenes2 database
biocore/BIRDMAn
Bayesian Inferential Regression for Differential Microbiome Analysis
biocore/qadabra
Snakemake workflow for comparison of differential abundance ranks
biocore/greengenes2
Processing support for Greengenes2
biocore/metagenomics_pooling_notebook
Jupyter notebooks to assist with sample processing
biocore/pynast
Python Nearest Alignment Space Termination tool (PyNAST): Official repository for software and unit tests
biocore/microsetta-private-api
A private microservice to support The Microsetta Initiative
biocore/american-gut-web
The website for the American Gut Project participant portal
biocore/improved-octo-waddle
Balanced parentheses succinct data structure in Python
biocore/micov
Aggregate genome coverage
biocore/mg-scripts
Knight Lab internal Metagenomic processing scripts for demultiplexing, QC and host removal
biocore/microsetta-interface
The Microsetta participant facing user interface
biocore/q2-katharoseq
biocore/unifrac-binaries
biocore/microsetta-admin
biocore/absquant
biocore/Cq-VIEW
A qPCR-based companion to the C-VIEW (COVID-19 VIral Epidemiology Workflow) pipeline that calculates samples' viral loads.
biocore/microsetta-processing
Processing scripts for The Microsetta Initiative
biocore/mustached-octo-ironman
Easy dispatched compute in a Tornado environment
biocore/q2-surpi
A QIIME 2 plugin that connects SURPI+ results to QIIME 2 for analysis