Single cell RNA-seq has enabled high-resolution characterization of molecular signatures of tumor-infiltrating lymphocytes. However, analyses at the transcript isoform level are rarely reported. As alternative splicing is critical to T cell differentiation and activation, here we proposed a computational method named as IDEA to comprehensively detect and annotate differentially used isoforms across cell subtypes.
This repository works as an example to reproduce figures in the article. The demo data, which contains the expression data of CD8+ T cells and transcripts of genes presented in the paper, is available in /demo/.
Run the codes in the following order:
- 01.calculateEnrichment.Rmd perform the enrichment analysis
- 02.Annotation_and_Event_detection.Rmd add functional and structural annotations to transcripts
- 03.plotEnrichmentofGenes.Rmd drawing the organized plot. A successful run results in plots like the one shown below.
