Tools for visualising microbial community amplicon data

Various functions for analysis of microbial community data

Metabolic modeling tutorial for EMBO practical course: Metabolite and species dynamics in microbial communities 2022

📦BEEM-Static: An R package for inferring microbial interactions based on Lotka-Volterra models

lake itag measurements over nineteen years

Environmental metagenomics, Spring 2022, Physalia Courses

A quick and user-friendly pipeline to go from raw fastq data from Illumina (paired-end sequencing) to processed ASVs and Taxonomic data.

Data and code for LaMartina et al., 2021

Supplemental code of the paper "Environmental selection shapes the formation of near-surface groundwater microbiomes".

Microbial co-occurrence network reveals climate and geographic patterns for soil diversity on the planet

Data and code for Kimbell et al., 2021

PubMed trend analysis of ecological keywords

Interactive and evolving catalogue of microbial interactions based on the framework of Pacheco and Segrè (2019)

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

QIIME 2 and R code along with manifests, metadata, inputs, and outputs for duckweed microbiome project (Acosta et al, 2020, Plos One).

Script repository related to the data processing and analyses of the study "Evidence of habitat specificity in sponge microbiomes from Antarctica"

This is a repository with my commonly-shared scripts.

Groundwater bacterial communities evolve over time, exhibiting cyclic similarity patterns in response to multi-annual recharge events

This repository contains all code used to perform the analysis presented in "Changes in the microbial communities of a tree fern along an elevation gradient"