Workflow and repository of scripts used for analysis in
Single-cell RNA sequencing of Plasmodium vivax sporozoites reveals stage- and species-specific transcriptomic signatures
Anthony A. Ruberto 1,#,^, Caitlin Bourke 2,3,#, Amélie Vantaux 4, Steven P. Maher 5, Aaron Jex 2,3, Benoît Witkowski 4, Georges Snounou 6, Ivo Mueller 1,2,3,*
1 Department of Parasites and Insect Vectors, Institut Pasteur, Paris, France
2 Division of Population Health and Immunity, Walter and Eliza Hall Institute of Medical Research, Parkville, Victoria, Australia
3 Department of Medical Biology, The University of Melbourne, Parkville, Victoria Australia
4 Malaria Molecular Epidemiology Unit, Institut Pasteur du Cambodge, Phnom Penh, Kingdom of Cambodia
5 Center for Tropical and Emerging Global Diseases, University of Georgia, Athens 30602, USA
6 Commissariat à l'Énergie Atomique et aux Énergies Alternatives-Université Paris Sud 11- INSERM U1184, Immunology of Viral Infections and Autoimmune Diseases (IMVA-HB), Infectious Disease Models and Innovative Therapies (IDMIT) Department, Institut de Biologie François Jacob (IBFJ), Direction de la Recherche Fondamentale (DRF), Fontenay-aux-Roses, France
# AAR and CB contributed equally to this work
^ Current address: Center for Tropical and Emerging Global Diseases, University of Georgia, Athens 30602, USA
* Corresponding author email: mueller@wehi.edu.au
🔍 This is a repository containing the Rmd files and scripts that were created for the analysis of Plasmodium vivax sporozoites.
🔑 There are several starting points if you would like to re-run the analysis:
- Raw sequencing files as stored at ENA
- requires re-mapping with STARsolo or your preferred mapping software
- STARsolo output stored at Zenodo
- reproducible workflow
- Rds (ie starting mid-way through) output stored at Zenodo
- reproducible workflow
- re-run a specific part of the analysis
The .Rmd files are numbered according to the figure panels they generate (ie 0_ = pre-processing, 1*_ = Fig1, 2*_ = Fig2 etc.)
