microbiome

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Here are 175 public repositories matching this topic...

torognes / vsearch

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Versatile open-source tool for microbiome analysis

search bioinformatics clustering metagenomics chimera fasta microbiome fastq metabarcoding amplicon sequence-alignment

Updated Nov 6, 2020
C++

biocore / qiime

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Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.

analysis microbiome

Updated Jan 23, 2018
Python

benjjneb / dada2

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Accurate sample inference from amplicon data with single nucleotide resolution

bioinformatics taxonomy metagenomics bioconductor microbiome metabarcoding amplicon

Updated Nov 2, 2020
R

microbiome / microbiome

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microbiome R package

r microbiology microbiome microbiome-analysis phyloseq human-microbiome population-study hitchip hitchip-atlas

Updated Oct 27, 2020
R

biocore / qiita

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Qiita - A multi-omics databasing effort

python microbiome microbiome-analysis

Updated Nov 8, 2020
Python

torognes / swarm

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A robust and fast clustering method for amplicon-based studies

bioinformatics clustering fasta sequence microbiome metabarcoding

Updated Sep 30, 2020
C++

benjjneb / decontam

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Simple statistical identification and removal of contaminants in marker-gene and metagenomics sequencing data

bioinformatics metagenomics microbiome metabarcoding amplicon contamination

Updated Jul 6, 2020
R

biocore / emperor

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Emperor a tool for the analysis and visualization of large microbial ecology datasets

visualization python bioinformatics microbiome ordination emperor biplots

Updated Oct 14, 2020
JavaScript

will-rowe / hulk

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Histosketching Using Little Kmers

hashing genomics sketching microbiome

Updated Jul 22, 2019
Go

cduvallet / microbiomeHD

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Cross-disease comparison of case-control gut microbiome studies

reproducible-research microbiome reproducible-paper

Updated Feb 2, 2019
Python

lch14forever / microbiomeViz

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Visualize microbiome data with black magic ggtree

visualization ggplot2 r microbiome ggtree

Updated Sep 3, 2020
R

MicrobeLab / DeepMicrobes

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DeepMicrobes: taxonomic classification for metagenomics with deep learning

bioinformatics deep-learning next-generation-sequencing metagenomics microbiome

Updated Feb 19, 2020
Python

rdpstaff / RDPTools

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Collection of commonly used RDP Tools for easy building

bioinformatics makefile microbiology microbiome bayesian-classifiers 16s sequence-alignment

Updated Apr 9, 2020
Makefile

shafferm / DRAM

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

bioinformatics annotation genomics metagenomics microbiome viral-genomics viral-metagenomics metagenome-assembled-genomes

Updated Oct 6, 2020
Python

nextgenusfs / amptk

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AMPtk: Amplicon ToolKit for NGS data (formally UFITS)

next-generation-sequencing amplicons microbiome mycobiome fungi rdna coi lsu co1 mtco1

Updated Oct 7, 2020
Python

Russel88 / DAtest

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Compare different differential abundance and expression methods

metagenomics rnaseq auc proteomics metabolomics microbiome false-positive-control differential-expression 16s otu marker-gene-analysis relative-abundances compare-methods differential-abundance-methods

Updated Jul 15, 2020
R

meringlab / FlashWeave.jl

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Inference of microbial interaction networks from large-scale heterogeneous abundance data

metadata bioinformatics julia metagenomics high-performance-computing microbiome probabilistic-graphical-models co-occurence compositional-data ecological-network

Updated Oct 26, 2020
Julia

gerberlab / mitre

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The Microbiome Interpretable Temporal Rule Engine

bioinformatics computational-biology statistical-analysis bayesian-inference microbiome

Updated Jan 30, 2020
Python

biocore / redbiom

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Sample search by metadata and features

bioinformatics microbiome qiime biom

Updated Aug 19, 2020
Python

FrederickHuangLin / ANCOM

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R scripts for Analysis of Composition of Microbiomes (ANCOM).

microbiome ancom

Updated Sep 20, 2020
R

JTFouquier / ghost-tree

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creating hybrid-gene phylogenetic trees for diversity analyses

python diversity bioinformatics python3 phylogenetic-trees phylogenetics microbiology microbiome fungi fungal microbial-ecology

Updated Feb 15, 2019
Python

micom-dev / micom

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Python package to study microbial communities using metabolic modeling.

python flux community modeling systems-biology biochemistry microbiome cobra microbiota cobrapy metabolic-models

Updated Aug 26, 2020
Python

BioJulia / Microbiome.jl

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For analysis of microbiome and microbial community data

biology julia-language logo microbiome ecology

Updated Aug 6, 2020
Julia

biocore / calour

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exploratory and interactive microbiome analyses based on heatmaps

bioinformatics heatmap jupyter-notebook microbiome exploratory

Updated Nov 4, 2020
Python

microsud / microbiomeutilities

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The is mostly a wrapper tool using phyloseq and microbiome R packages.

sequencing metagenomics microbial-communities microbiome amplicon 16s microbiome-analysis microbiome-data core-microbiome qc-pipeline

Updated Nov 7, 2020
R

SchlossLab / mothuR

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R package to work with mothur output files

rstats microbiome r-package mothur

Updated Oct 15, 2020
R

yiluheihei / microbiomeMarker

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R package for microbiome biomarker discovery

r metagenomics microbiome r-package biomarker-discovery lefse differential-abundance-analysis

Updated Oct 23, 2020
R

MetaSUB / MetaSUB_CAP

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A comprehensive pipeline for short read metagenomic data

bioinformatics pipeline metagenomics bioinformatics-pipeline microbiome

Updated Aug 25, 2020
Python

biobakery / melonnpan

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Model-based Genomically Informed High-dimensional Predictor of Microbial Community Metabolic Profiles

workflow machine-learning tools public metagenomics bioconductor microbial-communities metabolomics microbiome multi-omics relative-abundances biobakery metabolite-prediction mallick metabolite-compounds

Updated Nov 7, 2020
R

mibwurrepo / Microbial-bioinformatics-introductory-course-Material-2018

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Course material for OPEN & REPRODUCIBLE MICROBIOME DATA ANALYSIS SPRING SCHOOL

microbiome wageningen-university teaching-materials microbiota

Updated May 1, 2020
R

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microbiome

Here are 175 public repositories matching this topic...

torognes / vsearch

biocore / qiime

benjjneb / dada2

microbiome / microbiome

biocore / qiita

torognes / swarm

benjjneb / decontam

biocore / emperor

will-rowe / hulk

cduvallet / microbiomeHD

lch14forever / microbiomeViz

MicrobeLab / DeepMicrobes

rdpstaff / RDPTools

shafferm / DRAM

nextgenusfs / amptk

Russel88 / DAtest

meringlab / FlashWeave.jl

gerberlab / mitre

biocore / redbiom

FrederickHuangLin / ANCOM

JTFouquier / ghost-tree

micom-dev / micom

BioJulia / Microbiome.jl

biocore / calour

microsud / microbiomeutilities

SchlossLab / mothuR

yiluheihei / microbiomeMarker

MetaSUB / MetaSUB_CAP

biobakery / melonnpan

mibwurrepo / Microbial-bioinformatics-introductory-course-Material-2018

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