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
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Updated
Oct 27, 2023 - R
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
Machine learning for microbiome data
genome annotation analyzer for the microbiome analysis
Convert the American Gut Microbiome Project phenotype .xml files into a single .csv file.
This repository contains R scripts for data analyses and visualization.
short-read amplicon data visualization suite
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.
Repository for the data associated with my masters thesis
Analyzing microbiome data from Gigante, Barro Colorado, Panama. Part of an Undergraduate Thesis (defended on May 13th, 2022).
Python utility to generate distance matrices, perform PCoAs and generate taxonomic summaries using simple tab-separated feature tables.
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.
This is the data and R code associated with our paper "A t-SNE Based Classification Approach to Compositional Microbiome Data"
Microbiome Diversity Inspector - A platform for visual analysis of microbiome data.
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.
A Shiny interface for the MicrobiomeStat R package, designed to facilitate analysis and visualization of microbiome data.
Code to reproduce the analyses from the paper "Benchmarking microbiome transformations favors experimental quantitative approaches to address compositionality and sampling depth biases"
A database for storing and analyzing omics data
Exploring different database implementations for clinical microbiome data
MicrobiomeStat Tutorial Repository: This is a comprehensive resource for learning how to use the MicrobiomeStat package. It provides a step-by-step guide to effectively analyze complex microbiome data.
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