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nf-core /ampliseq

Star194

Amplicon sequencing analysis workflow using DADA2 and QIIME2

workflow pipeline nextflow metagenomics pacbio edna microbiome iontorrent illumina metabarcoding 16s rrna its 18s taxonomic-classification amplicon-sequencing qiime2 nf-core taxonomic-profiling

UpdatedMar 12, 2025
Nextflow

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.

ctf microbiome rpca qiime2 compositional-data-analysis rclr joint-rpca tempted

UpdatedOct 1, 2024
Python

biocore /empress

Star51

A fast and scalable phylogenetic tree viewer for microbiome data analysis

visualization bioinformatics microbiome ordination phylogeny qiime biplot qiime2 tree-plot

UpdatedAug 4, 2024
JavaScript

sbslee /dokdo

Sponsor

Star44

A Python package for microbiome sequencing analysis with QIIME 2

visualization api cli qiime2 microbiome-sequencing-analysis

UpdatedJan 28, 2024
Python

cafferychen777 /MicrobiomeStat

Star39

Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat

visualization statistics longitudinal-data microbiome omics metagenomes metagenomic-analysis microbiome-analysis phyloseq dada2 omics-data-integration amplicon-sequencing microbiome-data qiime2 16s-rrna microbiome-workflow

UpdatedFeb 17, 2025
R

Gibbons-Lab /isb_course_2022

Star27

Materials and presentation for the 2022 ISB Microbiome course.

analysis systems-biology sequencing microbiome metabolic-models microbial-ecology qiime2 16s-seq

UpdatedJun 13, 2024
Jupyter Notebook

Gibbons-Lab /isb_course_2023

Star24

Materials and presentation for the 2023 ISB Microbiome course.

analysis systems-biology sequencing microbiome hacktoberfest metabolic-models microbial-ecology qiime2 pathogens 16s-seq

UpdatedSep 25, 2024
Jupyter Notebook

olabiyi /snakemake-workflow-qiime2

Star16

Snakemake pipeline for 16S, 18S and ITS metagenomics using qiime2

conda microbiome qiime2 picrust2

UpdatedJan 20, 2024
Python

mghotbi /DspikeIn

Star10

The importance of converting relative to absolute abundance in the context of microbial ecology: Introducing the user-friendly DspikeIn R package

visualization phylogenetic-trees transformation gene-copies amplicon-sequencing qiime2 quantifying whole-cell spike-ins absolute-abundances

UpdatedMar 12, 2025
R

micom-dev /q2-micom

Star10

A Qiime plugin for MICOM.

hacktoberfest metabolic-models qiime2 16s-seq

UpdatedMar 4, 2025
Python

biomarv /16S-rRNA-gene-analysis-using-QIIME2

Star6

QIIME2 worklflow. From raw data to a feature table.

fastq-files amplicon-sequencing qiime2 16s-rrna

UpdatedSep 6, 2024

telatin /qax

Star5

Qiime2 Artifact eXtractor

metadata bioinformatics bioconda artifacts metabarcoding bioinfo qiime2 qax qiime2-installation

UpdatedJun 21, 2024
Nim

gibsramen /evident_

Star5

Effect size calculations for microbiome data

visualization python statistics data-visualization microbiome qiime2

UpdatedApr 26, 2022
Python

EmoryIntegratedComputationalCore /Methods

Star5

Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.

rna-seq notebook bioconductor deseq2 methods rna-seq-analysis edger omics-experiments ldm microbiome-analysis phyloseq rna-seq-pipeline emory qiime2 bayseq qvalue discovery-rates comparison-groups analytical-processes

UpdatedMar 21, 2023
R

BryanAbuchery /16S-rRNA-End-to-End-Analysis

Star4

Qiime2 and DADA2 are one of the latest bioinformatics tools used in 16S RNA analysis. The current Qiime2 and DADA2 pipelines support End to End 16S RNA analysis, among other analyses.

dada2 fastqc qiime2 rna-analysis mock-analysis