differential-abundance-analysis

R package for microbiome biomarker discovery

MaAsLin2: Microbiome Multivariate Association with Linear Models

Differential abundance (DA) and correlation analyses for microbial absolute abundance data

Archive: Data, scripts, and outputs for the Nat. Comm. paper "Analysis of Composition of Microbiomes with Bias Correction". Please check our ANCOMBC R package for the most up-to-date ANCOM-BC function.

Differential analysis of multi-omics data based on the Tweedie distribution

A manuscript exploring the effects of taxonomic bias on microbiome differential-abundance analysis.

Data, scripts, and outputs for the npj Biofilms and Microbiomes paper "Analysis of microbial compositions: A review of normalization and differential abundance analysis"

Large-scale Benchmarking of Microbial Multivariable Association Methods

dar: runs multiple differential abundance analysis methods and through a consensus strategy returns a set of differentially abundant features.

Collection of walkthrough tutorials on how to use Tweedieverse for differential analysis of omics data.

🦠Research project in Bioinformatics Institute 2023-2024

Large-scale Benchmarking of Microbial Multivariable Association Methods

A Bayesian model for the differential abundance analysis of microbiome sequencing data

An End-to-End GUI for real-time taxon identification via barcoded nanopore amplicon sequencing data. The pipeline is built using R Shiny library and majorly targets users with minimal coding background. Users can get from sequencing to results in a few clicks.

MAPping METastases in Neuroblastoma - spatially and temporally

Secondary analysis of Proteomics data in R, developed by the University of Arkansas for Medical Sciences for the NIH NIGMS Sandbox project.

Code and statistical explanations for commonly used microbiome analyses

Benchmarking DESeq2, MaAsLin2, and ANCOM-BC2 on simulated microbiome data with known differential taxa.

16S sequencing analysis pipeline for low biomass samples