Analyses of the Pristina leidyi cell type atlas manuscript
This is the code repository of the manuscript "Álvarez-Campos P, García-Castro H, Emili E, Pérez-Posada A, Salamanca-Díaz D, Mason V, Metzger B, Bely AE, Kenny N, Özpolat BD, and Solana J: Annelid adult cell type diversity and their pluripotent cellular origins".
Current version of the manuscript: https://www.biorxiv.org/content/10.1101/2023.04.25.537979v1
Here you can find all the code that was used to generate the main and supplementary figures of the manuscript. Some additional data such as Pseudobulk count matrices, GO term annotation, and WGCNA module membership can also be found here.
Most of the analyses are coded in Python using Jupyter notebooks, followed by R in RMarkdowns.
- Code for the main figures is found at
./Pristina_cell_type_atlas_Figures/. - Notebooks in the root directory of the repository were used to process the gene x cell matrix from scratch.
- Code for the "transcriptional landscape" analyses is found at
./pristina_transcriptomic_landscape/. - The rest of the folders contain a number of tables and plots to generate the different supplementary figures.
All analyses were run using Python v3 and R v4.0.3 in Windows OS 8 and Ubuntu GNU/Linux. All packages used are fully described in the Methods section of our manuscript.