microbiome

There are 22 repositories under microbiome topic.

torognes / vsearch
Versatile open-source tool for microbiome analysis
metabarcoding metagenomics chimera bioinformatics fastq fasta microbiome amplicon sequence-alignment clustering search
Language:C++ 627
benjjneb / dada2
Accurate sample inference from amplicon data with single nucleotide resolution
amplicon bioconductor bioinformatics metabarcoding metagenomics microbiome taxonomy
Language:R 446
biocore / qiime
Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
microbiome analysis
Language:Python 284
microbiome / microbiome
microbiome R package
microbiome microbiology microbiome-analysis r phyloseq human-microbiome population-study hitchip hitchip-atlas
Language:R 272
WrightonLabCSU / DRAM
Distilled and Refined Annotation of Metabolism: A tool for the annotation and curation of function for microbial and viral genomes
bioinformatics genomics metagenome-assembled-genomes metagenomics viral-genomics viral-metagenomics annotation microbiome
Language:Python 232
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
metagenomics computational-biology metabolic-models gut-microbiome snakemake metagenome-assembled-genomes mags metabolism bioinformatics flux-balance-analysis genome-scale-metabolic-model metabolic-modeling microbial-ecology microbiome systems-biology
Language:Python 165
yiluheihei / microbiomeMarker
R package for microbiome biomarker discovery
microbiome biomarker-discovery lefse metagenomics r differential-abundance-analysis r-package
Language:R 161
YuLab-SMU / MicrobiotaProcess
:microbe: A comprehensive R package for deep mining microbiome
microbiome microbiome-analysis microbiome-data rstats
Language:R 159
nf-core / ampliseq
Amplicon sequencing analysis workflow using DADA2 and QIIME2
amplicon-sequencing 16s nf-core nextflow pipeline workflow metagenomics rrna 18s its metabarcoding qiime2 edna taxonomic-classification illumina iontorrent microbiome pacbio taxonomic-profiling
Language:Nextflow 156
HumanMicrobiome
MaximilianKohler / HumanMicrobiome
Human Microbiome wiki
health microbiome science
152
benjjneb / decontam
Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data
microbiome bioinformatics contamination metagenomics amplicon metabarcoding
Language:R 137
genular / pandora
PANDORA - Predictive Analytics aNd Data Oriented Research Applications :computer:
machine-learning systems-biology data-science data-visualization data-mining pandora bioinformatics biomarkers clinical-data clustering data-integration drug-discovery genomic-data-analysis microbiome predictive-analytics transcriptomics tsne umap unsupervised-machine-learning
Language:Vue 132
qiita-spots / qiita
Qiita - A multi-omics databasing effort
microbiome microbiome-analysis python
Language:Python 119
torognes / swarm
A robust and fast clustering method for amplicon-based studies
metabarcoding clustering bioinformatics microbiome sequence fasta
Language:C++ 119
biobakery / Maaslin2
MaAsLin2: Microbiome Multivariate Association with Linear Models
biobakery public tools bioconductor microbiome metagenomics differential-abundance-analysis false-discovery-rate repeated-measures multiple-covariates
Language:R 102
grimmlab / MicrobiomeBestPracticeReview
Current Challenges and Best Practice Protocols for Microbiome Analysis using Amplicon and Metagenomic Sequencing
microbiome microbiome-analysis microbiome-workflow biomedical best-practices pipeline bioinformatics amplicon-sequencing assembly 16s-rrna metagenomics
Language:Shell 100
FrederickHuangLin / ANCOMBC
Differential abundance (DA) and correlation analyses for microbial absolute abundance data
ancom differential-abundance-analysis microbiome normalization sequencing correlation secom ancombc ancombc2
Language:R 90
nf-core / taxprofiler
Highly parallelised multi-taxonomic profiling of shotgun short- and long-read metagenomic data
metagenomics profiling taxonomic-profiling shotgun nf-core nextflow workflow pipeline classification microbiome taxonomic-classification long-reads nanopore bioinformatics illumina pathogen
Language:Nextflow 90
david-barnett / microViz
R package for microbiome data visualization and statistics. Uses phyloseq, vegan and the tidyverse. Docker image available.
microbiome microbiome-analysis microbiota rstats r
Language:R 89
ggpicrust2
cafferychen777 / ggpicrust2
Make Picrust2 Output Analysis and Visualization Easier
picrust2 functional-data metagenomic-analysis visualization tax4fun2 16s-rrna metagenomics microbiome microbiota
Language:R 81
MicrobeLab / DeepMicrobes
DeepMicrobes: taxonomic classification for metagenomics with deep learning
deep-learning metagenomics next-generation-sequencing bioinformatics microbiome
Language:Python 79
micom-dev / micom
Python package to study microbial communities using metabolic modeling.
microbiota cobrapy modeling metabolic-models flux biochemistry systems-biology microbiome python cobra community hacktoberfest
Language:Python 78
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
metagenomics bioinformatics k-mer bloom-filter microbiome minimizers taxonomy genbank gtdb ncbi refseq
Language:Python 78
microbiome / OMA
Orchestrating Microbiome Analysis
microbiome microbiome-analysis-book r bioconductor
Language:TeX 71
sccomp
stemangiola / sccomp
Testing differences in cell type proportions from single-cell data.
bayesian composition cytof microbiome r-package single-cell proportions batch-correction differential-proportion unwanted-variation multilevel random-effects
Language:R 70
lch14forever / microbiomeViz
Visualize microbiome data with black magic ggtree
microbiome ggplot2 ggtree r visualization
Language:R 67
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.
microbiome microbiome-analysis
Language:R 67
meringlab / FlashWeave.jl
Inference of microbial interaction networks from large-scale heterogeneous abundance data
metagenomics microbiome probabilistic-graphical-models high-performance-computing compositional-data metadata ecological-network co-occurence julia bioinformatics
Language:Julia 66
cduvallet / microbiomeHD
Cross-disease comparison of case-control gut microbiome studies
reproducible-paper reproducible-research microbiome
Language:Python 65
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.
rpca ctf qiime2 rclr compositional-data-analysis microbiome joint-rpca tempted
Language:Python 64
qiyunzhu / woltka
Woltka: a versatile meta'omic data classifier
bioinformatics metagenomics microbiome
Language:Python 64
AncientMetagenomeDir
SPAAM-community / AncientMetagenomeDir
Repository containing lists of all published ancient metagenomic (and related) samples and libraries
dataset metadata metagenomics-data archaeology palaeogenomics ancient-dna metagenomics microbiome pathogen sedadna
Language:HTML 63
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.
ancom microbiome
Language:R 56
will-rowe / hulk
Histosketching Using Little Kmers
sketching hashing genomics microbiome
Language:Jupyter Notebook 55
biocore / emperor
Emperor a tool for the analysis and visualization of large microbial ecology datasets
microbiome visualization emperor python bioinformatics ordination biplots
Language:JavaScript 52
rdpstaff / RDPTools
Collection of commonly used RDP Tools for easy building
16s bioinformatics microbiome microbiology bayesian-classifiers sequence-alignment
Language:Makefile 49

microbiome

torognes / vsearch

benjjneb / dada2

biocore / qiime

microbiome / microbiome

WrightonLabCSU / DRAM

franciscozorrilla / metaGEM

yiluheihei / microbiomeMarker

YuLab-SMU / MicrobiotaProcess

nf-core / ampliseq

MaximilianKohler / HumanMicrobiome

benjjneb / decontam

genular / pandora

qiita-spots / qiita

torognes / swarm

biobakery / Maaslin2

grimmlab / MicrobiomeBestPracticeReview

FrederickHuangLin / ANCOMBC

nf-core / taxprofiler

david-barnett / microViz

cafferychen777 / ggpicrust2

MicrobeLab / DeepMicrobes

micom-dev / micom

pirovc / ganon

microbiome / OMA

stemangiola / sccomp

lch14forever / microbiomeViz

zoecastillo / microbiomeExplorer

meringlab / FlashWeave.jl

cduvallet / microbiomeHD

biocore / gemelli

qiyunzhu / woltka

SPAAM-community / AncientMetagenomeDir

FrederickHuangLin / ANCOM-Code-Archive

will-rowe / hulk

biocore / emperor

rdpstaff / RDPTools