borenstein-lab

borenstein-lab's repositories

microbiome-metabolome-curated-data

Language:HTMLMIT48 3 6

burrito

A visualization tool for exploratory data analysis of metagenomic data

Language:JavaScriptGPL-3.035 11 36

fishtaco

FishTaco (Functional Shifts Taxonomic Contributors) is a metagenomic computational framework that aims to identify the driver taxa of microbiome functional shifts

Language:PythonNOASSERTION23 7 14

MIMOSA

Model-based Integration of Metabolite Observations and Species Abundances

Language:R23 9 2

MUSiCC

MUSiCC: A marker genes based framework for metagenomic normalization and accurate profiling of gene abundances in the microbiome

Language:PythonBSD-3-Clause15 8 12

CoMiDA

The code and distributable for designing minimal microbial communities with specified metabolic functions.

Language:C++NOASSERTION11 50

multi_view_integration_analysis

Language:R900

drug_microbiome

Data and code for paper "A data-driven approach for predicting the impact of drugs on the human microbiome"

Language:RGPL-3.07 60

MetaLAFFA

A bioinformatics pipeline for annotating functional capacities in shotgun metagenomic data with native compute cluster integration

Language:PythonGPL-3.07 5 12

empanada

empanada is a tool for evidence-based assignment of genes to pathways in metagenomic data

Language:PythonNOASSERTION3 6 3

microbiome-metabolome-evaluation

Language:R3 50

robustness_of_gut_microbiome-metabolite_associations

Language:R1 50

Multiomic analysis for the paper titled "Integrative analysis of untargeted serum and fecal metabolome and gut microbiome reveals a role in Crohn Disease and with signals that precede a disease flare"

Language:RGPL-3.0000

longitudinal_interpolation

Language:Jupyter Notebook000

robustness

Language:RGPL-3.006 1

SOURCE_multiomics

Language:RGPL-3.0000

T6SS

Language:Python050

vaginal_microbiome_manifold

Manifold detection