microbiome
There are 396 repositories under microbiome topic.
torognes/vsearch
Versatile open-source tool for microbiome analysis
benjjneb/dada2
Accurate sample inference from amplicon data with single nucleotide resolution
microbiome/microbiome
microbiome R package
biocore/qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
WrightonLabCSU/DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
franciscozorrilla/metaGEM
:gem: An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
nf-core/ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
YuLab-SMU/MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
yiluheihei/microbiomeMarker
R package for microbiome biomarker discovery
MaximilianKohler/HumanMicrobiome
Human Microbiome wiki
benjjneb/decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
genular/pandora
PANDORA :computer:
nf-core/taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
torognes/swarm
A robust and fast clustering method for amplicon-based studies
biobakery/Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
qiita-spots/qiita
Qiita - A multi-omics databasing effort
cafferychen777/ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
grimmlab/MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
FrederickHuangLin/ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
david-barnett/microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
MangiolaLaboratory/sccomp
Testing differences in cell type proportions from single-cell data.
micom-dev/micom
Python package to study microbial communities using metabolic modeling.
pirovc/ganon
ganon2 classifies genomic sequences against large sets of references efficiently, with integrated download and update of databases (refseq/genbank), taxonomic profiling (ncbi/gtdb), binning and hierarchical classification, customized reporting and more
microbiome/OMA
Orchestrating Microbiome Analysis
MicrobeLab/DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
jolespin/veba
A modular end-to-end suite for in silico recovery, clustering, and analysis of prokaryotic, microeukaryotic, and viral genomes from metagenomes
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.
meringlab/FlashWeave.jl
Inference of microbial interaction networks from large-scale heterogeneous abundance data
qiyunzhu/woltka
Woltka: a versatile meta'omic data classifier
zoecastillo/microbiomeExplorer
The Microbiome Explorer provides methods to analyze and visualize microbial community sequencing data either from the R command line or through a Shiny application. Written by Janina Reeder and Joseph N. Paulson.
cduvallet/microbiomeHD
Cross-disease comparison of case-control gut microbiome studies
lch14forever/microbiomeViz
Visualize microbiome data with black magic ggtree
SPAAM-community/AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
FrederickHuangLin/ANCOM-Code-Archive
Archive: R functions for Analysis of Composition of Microbiomes (ANCOM). Please check our ANCOMBC R package for the most up-to-date ANCOM function.
will-rowe/hulk
Histosketching Using Little Kmers
biocore/emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets