microbiome R package
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Updated
Aug 4, 2023 - R
microbiome R package
This repo contains the R microshades package, which contains a color blind accessible color palette with 30 unique colors and functions for applying these colors to microbiome data.
16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Demo: https://ycl6.github.io/16S-Demo/
Track, Analyze, Visualize: Unravel Your Microbiome's Temporal Pattern with MicrobiomeStat
Fantaxtic - Nested Bar Plots for Phyloseq Data
A comprehensive and customizable R package for microbiome analysis.
A model-based visualization method for microbiome data
accessory functions for processing microbial community data
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
Mothur procedures for 16S and ITS analysis
Working Demo on 16S rDNA V3-V4 amplicon sequencing analysis using dada2, phyloseq, LEfSe, picrust2 and other tools. Visit repo website for HTML output
R scripts used for the analysis of microbiomes associated with stony coral tissue loss disease (SCTLD) in the Florida Reef Tract
A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
Some of the analytical processes and tools we use to provide rigorous and actionable results to our clients.
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.
R package for analyzing microbial co-occurences
A simple R package to convert MetaPhlAn 4 output profiles to a phyloseq object.
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