Stars
🤝 Tool for mining KEGG pathways completeness data from eggNOG-mapper annotations
Classification of Eukaryotic and Prokaryotic sequences from metagenomic datasets
Classify metagenomic contigs as eukaryotic or prokaryotic
An analysis and visualization platform for 'omics data
Penn-State-Microbiome-Center / KickStart-Workshop-2025
Forked from Penn-State-Microbiome-Center/KickStart-Workshop-2024Materials for the 2025 PSU One Health Microbiome Center KickStart Workshop, August 5 - 18
Functions needed to run the GutMicro_16S_pipeline
Template for the current pipeline for further analyses of the output from our raw data pipeline (DF_GMH_pipeline)
Data analysis of bacterial communities associated with Rhopilema nomadica blooms, the predominant jellyfish in the Eastern Mediterranean Sea
Modeling whole bacterial genome as a sequence of proteins.
The ECOSYS model for terrestrial ecosystem biogeochemistry
An efficient and objective tool for optimizing microbiome rRNA gene trimming parameters
16S taxonomy assignment using an ecosystem-specific database.
tree visualization for tree + annotation data
From annotated genomes to metabolic screening in large scale microbiotas
A versatile and scalable algorithm for rogue taxon identification. Also includes implementations of the maximum agreement subtree, leaf stability index and taxonomic instability index
Examples of analyzing microbiome data in Goolge Colab
genEra is a fast and easy-to-use command-line tool that estimates the age of the last common ancestor of protein-coding gene families.
Universal and efficient structure-based core gene phylogeny with Foldseek and ProstT5
HGTector2: Genome-wide prediction of horizontal gene transfer based on distribution of sequence homology patterns.
R package to perform sensitivity analysis for comparative methods
Instantaneous Metagenome Taxonomic Profiling with MetaKSSD
Protologgger is a tool for the description of novel taxa by providing taxonomic, functional and ecological insights
Code repository of the Earth Microbiome Project.