Marine Ecology & Biodiversity

Practicals: exploring planktonic communities in the Tara Oceans

Instructor: Pedro C. Junger

This repo includes:

This repo contains the R Markdown script and the outputs for the practical session of the Marine Ecology & Biodiversity course as part of the PSL-Week. The aim of this tutorial is providing the students a toolbox to explore the Tara Oceans datasets to study plankton diversity in the global ocean. The example dataset is the Tara Oceans 18SV4 data processed by the swarm pipeline, but the current script should be easily adaptable to other datasets.

Datasets:

The example OTU and taxonomy tables are available here: https://zenodo.org/records/7235995, while the contextual data is here: https://zenodo.org/records/7229815.

• TARA-Oceans_18S-V4_Swarm-Mumu_table.tsv: OTU table
• TARA-Oceans_18S-V4_Swarm-Mumu_taxo.tsv: taxonomy of the OTU table
• context_general.tsv: Tara Oceans contextual data
• context_stat.tsv: Tara Oceans environmental data