Genome modeling and design across all domains of life

A newly developed metabolic modeling pipeline, SuperCC, which could simulate the performances of different microbiomes.

Interpretation and visualization of microbiome charts

Python package to study microbial communities using metabolic modeling.

💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data

CarveMe: genome-scale metabolic model reconstruction

The bookdown version lives here: https://bookdown.org/content/3890

A full-featured utility for managing Windows Subsystem for Linux (WSL)

customizable pipeline to identify viral sequences from (meta)genomic data

Simple GO Enrichment Analysis

Pipeline for metabolic annotation of microbial genomes

KrakenTools provides individual scripts to analyze Kraken/Kraken2/Bracken/KrakenUniq output files

📦 R package to compute functional diversity indices efficiently

R package for plotting Whittaker biomes with ggplot2

Bioinformatics program inStrain

Diversity Metrics Calculations for Rasterized Data

Mixed Models for Repeated Measures (MMRM) in R.

Snakemake workflow for metagenomic classification with Kraken2

Tool for recognizing genetic codes (incl. multiple genetic codes in phage genomes) and genetic-code-informed annotation of coding regions in prokaryotic sequences

A pipeline for the macro- and micro-diversity analyses and visualization of metagenomic-derived populations

A comparative genomics workflow using Nextflow, conda, Julia and R

🦠🧬 Unraveling Viral Genomes from Metagenomes

Predicting how Actic vegetation types distribution in 2050 based on CAVM and CMIP6 climate models

Visualising and reprojecting CMIP6 data from nc files

A wrapper to identify, bin, classify, and predict host-viral relationship for viruses

Individual-based simulation of diversification with Lotka-Volterra competition on an island