Processing NEON soil microbe marker gene sequence data into ASV tables.
Data and R analysis (diversity indices, PCA, correlation & chord networks) for metolachlor phytoremediation soil-microbiome metagenomics — JoX 2024 (DOI 10.3390/jox14030054)
QIIME 2 pipeline for 16S and ITS amplicon analysis of soil microbiome perturbation under antibiotic stress gradients (PRJEB95045).
Data and reconstructed R analysis (diversity indices, PCA, correlation networks) for sulfentrazone phytoremediation by Avena sativa — JoX 2025 (DOI 10.3390/jox15030087)
Microbiome analysis pipeline with reference tutorial. This code was written in October 2024 to process rRNA marker gene data (16S and ITS) from rhizosphere soil samples.
neonMicrobe: Processing NEON soil microbe marker gene sequence data into ASV tables, duplicated from https://github.com/claraqin/neonMicrobe
The R-Shiny application for the Australian Soil Microbial 16S data browsing.
Reproducible 16S rRNA amplicon sequencing workflow for Illumina MiSeq soil microbiome analysis.
Script for analyzing metabolic data
Adaption of Section 2 of Norgen's Soil DNA Isolation Kit. It was divided into 3 protocols, but feel free to wrap up (just pay attention to the number of tip racks). Recalibrate each time you are running the protocols (specially before the 3rdprotocol)
Biome Makers — independent third-party profile of a public API surface, by API Evangelist. Biome Makers is a global agricultural technology company founded in 2015 and headquartered in El Macero, California, that uses soil microbiome DNA sequencing and machine learning to measure and restore soil health.
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