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microbiomedata
nmdc-schema

National Microbiome Data Collaborative (NMDC) unified data model

8K 46 10
micom-dev
micom

Microbial community modeling based on cobrapy.

4K 127 23
shafferm
dram-bio

Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes

3K 332 62
cfrioux
miscoto

Python package for large-scale community selection in microbiota

2K 9 0
segrelab
micone

The Microbial Co-occurrence Network Explorer

2K 21 4
biocore
emperor

Emperor

1K 54 48
wwood
singlem

Novelty-inclusive microbial (and now dsDNA phage) community profiling of shotgun metagenomes

853 185 23
biocore
redbiom

Sample search by metadata and features

828 48 18
GRONINGEN-MICROBIOME-CENTRE
microberx

MicrobeRX

807 17 4
lozuponelab
amon-bio

Annotation of Metabolite Origin via Networks: A tool for predicting putative metabolite origins for microbes or between microbes and host with or without metabolomics data

737 26 11
nextgenusfs
amptk

AMPtk: amplicon tool kit

681 39 14
qiyunzhu
woltka

versatile meta-omic data classifier

542 79 25
biocore
qurro

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

523 34 10
amnona
dbbact-calour

dbBact (https://dbbact.org) interface for Calour (https://github.com/biocore/calour) for microbiome 16S analysis

493 1 0
JelenaBanjac
microbiome-toolbox

Early Life Microbiome Toolbox

432 12 2
metageni
superfocus

SUPER-FOCUS: A tool for agile functional analysis of shotgun metagenomic data

309 24 12
biocore
empress

Fast and scalable phylogenetic tree viewer for multi-omic data analysis

283 55 32
gerberlab
mitre

The Microbiome Interpretable Temporal Rule Engine

243 46 4
metageni
metagenomics-focus

FOCUS: An Agile Profiler for Metagenomic Data

234 10 8
korem-lab
pymgpipe

Python implementation of mgpipe

229 7 1
jolespin
compositional

Python package for compositional data analysis including CLR/ILR, proportionality, partial correlation with basis shrinkage, and visualizations.

209 28 0
MiBiPreT
mibiscreen

A collection of analytical and semi-semianalytical solutions for hydrogeological transport phenomena

199 1 0
fredhutch
famli

Functional Analysis of Metagenomes by Likelihood Inferrence

192 17 2
smdabdoub
qiime-tools

Tools for phylogenetic data analysis including visualization and cluster-computing support.

180 15 3
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