NAISS
SUPR
NAISS Projects
SUPR
Bioinformatic Analysis and Data Integration of Unconventional T Cells and Gastroesophageal Cancer Datasets
Dnr:

NAISS 2025/22-1552

Type:

NAISS Small Compute

Principal Investigator:

Angeline Enton Raj

Affiliation:

Karolinska Institutet

Start Date:

2025-11-13

End Date:

2026-12-01

Primary Classification:

30110: Immunology in the Medical Area

Webpage:

Allocation

Abstract

This project aims to perform large-scale bioinformatic and computational analyses of high-dimensional sequencing datasets derived from two ongoing Bianca projects: (1) Multi-layered characterization of human double-negative αβ T cells (DNTs), and (2) GEAC multiomic characterization. Both studies generate multi-omic data, including bulk RNA-seq, single-cell RNA/TCR-seq, CITE-seq, and spatial data. While raw data are stored and processed securely on Bianca, secondary and exploratory analyses such as R/Python-based data visualization, integration, and downstream pathway analyses will be conducted on Dardel, where internet access allows convenient installation of new packages and external dependencies. The project will utilize Dardel’s computational resources primarily for R- and Python-based workflows (Seurat, scRepertoire, SPIAT, CellChat, NicheNet, clusterProfiler, DandelionR etc.), exploratory modeling, and integrative analysis of immune cell subsets in cancer and health.