This repository contains all code necessary to reproduce results of pseudobulk analysis showed in : paper.
# Usage
# Usage
## 1. Download datasets
* Smilie_2019 : from [Christopher S. Smillie, et al. 2019](https://doi.org/10.1016/j.cell.2019.06.029) available on the Single Cell Portal [SCP259](https://singlecell.broadinstitute.org/single_cell/study/SCP259/intra-and-inter-cellular-rewiring-of-the-human-colon-during-ulcerative-colitis#study-summary).
* Kong_2023 : from [Lingjia Kong, et al. 2023](https://doi.org/10.1016/j.immuni.2023.01.002) available on the Single Cell Portal [SCP1884](https://singlecell.broadinstitute.org/single_cell/study/SCP1884/human-cd-atlas-study-between-colon-and-terminal-ileum#study-summary).
...
...
@@ -19,3 +16,25 @@ The second one uses both Seurat and DESeq2 to uncover wether ICAM-1 is different
Please note to write your own paths to the datasets before running.
# Reference
**Role of ICAM-1 in the Adhesion of T cells to Enteric Glia: Perspectives in the Formation of Plexitis in Crohn’s disease**
*Short title:* ICAM-1 in enteric glia/T cells interaction
Authors: Julie Pabois1, Tony Durand1, Catherine Le Berre1, Rhiannon T. Filippone3, Théo Noël1, Emilie Durieu1, Céline Bossard2, Sarah Bruneau3, Malvyne Rolli-Derkinderen1, Kulmira Nurgali4,5,6, Michel Neunlist1, Arnaud Bourreille1, Isabelle Neveu1, Philippe Naveilhan1.
Institutions :
1. Nantes Université, CHU Nantes, Inserm, TENS, The Enteric Nervous System in Gut and Brain Diseases, IMAD, Nantes, France
2. Service d’Anatomie et Cytologie Pathologique, Inserm, CRCINA, Université de Nantes, CHU Nantes, Nantes, France
3. CHU Nantes, Nantes Université, INSERM, Center for Research in Transplantation and Translational Immunology, UMR 1064, F-44000, Nantes, France
4. Institute for Health and Sport, Victoria University, Melbourne, VIC, Australia
5. Department of Medicine Western Health, The University of Melbourne, Melbourne, Australia
6. Regenerative Medicine and Stem Cell Program, Australian Institute for Musculoskeletal Science (AIMSS), Melbourne, Australia
This repository contains all code necessary to reproduce results of pseudobulk analysis showed in : paper.
