💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
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Updated
Jan 12, 2024 - Python
💎 An easy-to-use workflow for generating context specific genome-scale metabolic models and predicting metabolic interactions within microbial communities directly from metagenomic data
Tools for visualising microbial community amplicon data
creating hybrid-gene phylogenetic trees for diversity analyses
Various functions for analysis of microbial community data
Materials and presentation for the 2022 ISB Microbiome course.
Materials and presentation for the 2023 ISB Microbiome course.
📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models
Comparative Metatranscriptomics Workflow
Easy-to-use tool facilitating work with Mothur.
Environmental metagenomics, Spring 2022, Physalia Courses
A simple package for simulations of microbial growth experiments with realistic sources of error.
Scripts for a manuscript titled "Subsurface Microbial Communities Reflect Regional-Scale Groundwater Hydraulic Connectivity" (submitted)
Full-length bacterial 16S rRNA marker genes from a diverse wastewater sample set. LaMartina, et al., ASM Resource Announcement, 2022
My personal research website
Environmental metagenomics, Spring 2023, Physalia Courses
Application of DEMENTpy to a climate gradient in Southern California
Description of the metagenomic pipeline we have for analysis of 16S and 18S amplicon NGS
Data and code for LaMartina et al., 2021
Data and code for Kimbell et al., 2021
Super snazzy online phylogenetic tree viewer with automatic customization using simple, tab-separated text files.
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