Docker RStudio container for Duke University IBIEM 2017 - Integrative Bioinformatics for Investigating & Engineering Microbiomes
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Updated
May 8, 2018 - Shell
Docker RStudio container for Duke University IBIEM 2017 - Integrative Bioinformatics for Investigating & Engineering Microbiomes
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.
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)
A python implementation of the decontam R package for ASV filtering.
Analysis of Multiple Circadian/Longitudinal Datasets
Generic code for performing microbiome-wide association studies with a variety of models
MAPle provides three different modules for the analysis of paired-end short read metagenomic data
Microbiome Data Analysis
Identifying gut microbiome features associated with the risk of acquiring an enteric drug-resistant organism (e.g. vancomycin-resistant Enterococcus and resistant gram-negative bacteria) in patients recently discharged from acute-care hospital and admitted into nursing homes.
Infer network from count data within Snakemake using a sparse Poisson lognormal model (PLNnetwork)
A python package to calculate the dysbiosis score in microbiome datasets
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.
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