Shiny app to easily create publishable plots for scientific papers

https://www.cell.com/cell-reports/fulltext/S2211-1247(24)01418-9?_returnURL=https%3A%2F%2Flinkinghub.elsevier.com%2Fretrieve%2Fpii%2FS2211124724014189%3Fshowall%3Dtrue

deveolpmental stage

codes from paper https://www.nature.com/articles/s41564-024-01739-1

paper code from https://doi.org/10.1038/s41467-024-48355-5 Alex-Mohr n Corrie Whisner, intermittent fasting versus continuous caloric restriction

codes from https://www.tandfonline.com/doi/epdf/10.1080/19490976.2023.2292254?needAccess=true

this tool is to analyze longitudinal microbiome data

Fungal shotgun metagenomic profiling; taxonomic and functional

Generally-healthy individuals with aberrant bowel movement frequencies show enrichment for microbially-derived blood metabolites associated with impaired kidney function.

Code and files for the main nf-core website.

differential analyses tool from Knight lab

Efficient Python Tricks and Tools for Data Scientists

Fast expectation maximization for microbial source tracking

Plugin for analysing the efficacy of fecal microbiota transplants

ancient oral microbiomes with some good taxonomy figures

qiime2 plugin for ANCOMBC

Nextflow pipeline to analyze PacBio HiFi full-length 16S data

R package for microbiome analysis. Provides helper functions for common workflows ranging from preprocessing to visualization.

Collection of useful data science topics along with code and articles

Multi-Omics Factor Analysis

R package for searching, downloading and analysis of EBI MGnify metagenomics data

🐝 Awesome R packages that offer extended UI or server components for the R web framework Shiny

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

Codes and Data corresponding to the meta-analysis investigating age-gut microbiome interactions in seven major microbiome data repositories

Omnibus and Maaslin2 Rscripts and hmp2-data for downstream analyis

An R package for data analysis in microbial community ecology

Metagenome CoAssembly scripts from Michael Pavia