The emergence of large single cell RNA-seq(scRNA-seq) datasets facilitates biological discoveries at single-cell resolution. The information encoded in single cell atlases should be readily accessible to users from all disciplines. The Hemberg lab has developed scfind, a search engine for gene expression patterns in cell atlases scfind.
scfindME is built on top of scfind and it adapts scfind to alternative splicing analysis. Through querying with splicing features or cell types, scfindME conducts rapid searching and returns feature-enriched cell types or cell type-specific splicing signatures, respectively. scfindME also discovers cell type-specific mutually exclusive exon pairs and clustered spliced-in or spliced-out of a block of exons by enumerating over all possible combinations of splicing events.
Quantification of single cell alternative splicing events is performed by Whippet integrated in the workflow MicroExonator. scfindME builds custom indices for any single-cell dataset using the output files of Whippet.
To install or run scfindME, use the following codes in an R session:
install.packages("devtools")
devtools::install_github("hemberg-lab/scfindME")
library(scfindME)
Please refer to the scfindME package Vignette for a detailed user guide.
Please contact Miss Yuyao Song (ys585@cam.ac.uk) for any enquiries or bug reports.