Microbiome Diversity Inspector - A platform for visual analysis of microbiome data.
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Updated
Jun 17, 2018 - JavaScript
Microbiome Diversity Inspector - A platform for visual analysis of microbiome data.
Convert the American Gut Microbiome Project phenotype .xml files into a single .csv file.
This is the data and R code associated with our paper "A t-SNE Based Classification Approach to Compositional Microbiome Data"
Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"
Python utility to generate distance matrices, perform PCoAs and generate taxonomic summaries using simple tab-separated feature tables.
Visualization of world-class repeated measures microbiome data from the lungs of children with Cystic Fibrosis, with wide-ranging applications to other longitudinal microbiome data.
I performed PCA and t-SNE on the microbiome dataset and visualized the data in 2D space. I also report what I learned from the PCA and t-SNE analyses.
A microbiome knowledge graph was constructed using data from the Human Microbiome Project, IBD cohort. This project was done as a part of my dissertation for my MSc in Health Data Science with The University of Manchester. It was done as an internship with Zifo RnD Solutions, a leading Scientific Informatics Company.
Analyses in R and Python Using curatedMetagenomicData
A list of R environment based tools for microbiome data exploration, statistical analysis and visualization
Machine learning for microbiome data
Analyzing microbiome data from Gigante, Barro Colorado, Panama. Part of an Undergraduate Thesis (defended on May 13th, 2022).
A project to evaluate the differences in bacterial association networks from rainforest and converted pasturelands in the Colombian Amazon region using CCLasso and SPRING inference methods
This repository contains R scripts for data analyses and visualization.
The scripts contained in this repository relate directly to the work conducted by the Tree Root Microbiome Project (TRMP) led by Dr Steve Wakelin.
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.
GDmicro - Use GCN and Deep adaptation network to classify host disease status based on human gut microbiome data.
A Bayesian model for the differential abundance analysis of microbiome sequencing data
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.
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