Compare different differential abundance and expression methods
Various functions for analysis of microbial community data
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
The is mostly a wrapper tool using phyloseq and microbiome R packages.
accessory functions for processing microbial community data
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
Mothur procedures for 16S and ITS analysis
code to reproduce AIH results
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
🌊 16S rRNA microbiome data analysis workflow using DADA2 and R on a high performance cluster using SLURM
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
A nextflow pipeline for the analysis of 16S amplicon data built around RExMap
Analysis scripts for Gortzia yakutica paper
Rsearch: An R Interface to VSEARCH supporting visualization and parameter tuning
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