A repository containing a demo microbiome workflow for R and Python
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Updated
Apr 11, 2018 - Jupyter Notebook
A repository containing a demo microbiome workflow for R and Python
🌊 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
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.
Reconstructing a dada2 pipeline with batch processing using an OOP design
Analysis of 16S rRNA (dada2 amplicon sequence variants) from human volunteers given various vaccines following two different antibiotics treatments compared to no antibiotics.
CUSO Microbiome analysis workshop 2020
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
Modified dada2 script, used for master's thesis project. Takes fast2 files and outputs ASV table, taxonomy table, phylogenetic tree, and input files for PICRUSt2
Collection of notebooks describing the basic analysis workflow for a 16S rRNA gene amplicon sequencing project
Microbiome Analysis Using R Workshop originally organized for the 2018 ASM General Meeting in Atlanta, GA, but regularly updated since.
A workflow for processing CCS reads of AMF to ASVs using DADA2
Docker convenience image containing R and the DADA2 package (plus dependencies), used for processing amplicon data.
neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe
This is repository of amplicon sequencing data and bioinformatics pipeline codes for the nectar microbiome of Monkey Flowers.
This repositorey contain the dada2 pipeline used to process the illumina sequence reads in the manuscript "Temporal variability in the growth-enhancing effects of different bacteria within the microbiome of the diatom Actinocyclus sp." (DOI: 10.3389/fmicb.2023.1230349)
Introduction to 16S Amplicon Sequencing Data Analysis using DADA2
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