This repository organizes the scripts, analyses, figures, and latex files associated with the publication entitled Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes (1).
We developed a Python package to implement the sparse tensor decomposition model used in the manuscript to analyze cyanobacterial gene expression data. The code for this package is published in a separate GitHub repository. Details on library usage can be found on the Barnacle documentation website. The documentation includes:
- An overview of tensors and tensor decomposition.
- A gallery of examples that demonstrate tensor analysis with Barnacle.
- An API reference of Barnacle modules.
For a more technical discussion of the sparse tensor decomposition model implemented in Barnacle, please see the Methods section of the paper.
All data needed to evaluate the conclusions in the paper can be found in this repository and the Supplementary Materials.
Supplementary Data files are available in an associated Zenodo repository.
The sequences reported have been deposited in the NCBI Sequence Read Archive under the following BioProject accession numbers:
- Gradients 1 (2016)
- PRJNA492143 (transect samples)
- Gradients 2 (2017)
- PRJNA816919 (transect samples)
- PRJNA1090086 (depth samples)
- PRJNA1090042 (20L nutrient incubations)
- PRJNA1088528 (4L sulfur incubations)
- Gradients 3 (2019)
- PRJNA1091352 (transect samples)
- PRJNA1090467 (depth samples)
- PRJNA1090899 (diel samples)
For an overview of the research in this manuscript, take a look at this poster we made about it:
- Blaskowski, Stephen, Marie Roald, Paul M. Berube, Rogier Braakman, and E. Virginia Armbrust. "Simultaneous acclimation to nitrogen and iron scarcity in open ocean cyanobacteria revealed by sparse tensor decomposition of metatranscriptomes." bioRxiv (2024): 2024-07. https://doi.org/10.1101/2024.07.15.603627.