Longitudinal OSA Experiments - Lesion, Microbiome, Metabolome
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Updated
Sep 18, 2020 - Jupyter Notebook
Longitudinal OSA Experiments - Lesion, Microbiome, Metabolome
A reference-free statistical approach to diversity-generating & mobile genetic element discovery
Workflow and R scripts for Giongo et al. (2024)
An interactive web application that provides a flexible graphical user interface (GUI) to the Reverse Ecology analysis package for R
Codes for the statistical analysis that investigates the impact of high-fat diet on gut microbiome and serotonergic gene expression in the raphe nuclei.
Reusing publicly available whole transcriptome data to determine the state of the microbiome at time of sampling.
A python implementation of the decontam R package for ASV filtering.
Analysis of Multiple Circadian/Longitudinal Datasets
Docker RStudio container for Duke University IBIEM 2017 - Integrative Bioinformatics for Investigating & Engineering Microbiomes
microbiome analysis of ant colonies
Vaginal microbiome data analysis using QIIME2 in women with gynecologic cancer.
Code to reproduce preprocessing analysis of IBD dataset from the Human Microbiome Project. This work will provide a walk through analysis tool for the scientific community with less technical knowledge on data science and machine learning.
In this repository live the bash, R and Julia scripts used to explore the microdiversity of the prokaryotic community at Uranouchi Inlet (9-sample time-series) by means of metagenomic shotgun sequencing under the supervision of the Ogata Lab.
Code and raw data for *Galaxea fascicularis* microbiome data analysis
The following codes are focused on microbiome analysis, alpha, beta and relative abundance differences.
A selection of analytical approaches, tools, and utilities for the processing of microbiome data derived from either 16S rRNA amplicon sequencing or shotgun metagenomics.
Generic code for performing microbiome-wide association studies with a variety of models
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