Longcell is a package for single cell/Visium spot alternative splicing analysis. It accepts the single cell/Visium spot isoform quantification from Longcell-pre, and gives the analysis of highly viarable isoform identification, differential alternative splicing.
Installation
The easiest way to get Longcell is to install it from Github:
# install.packages("devtools")
devtools::install_github("yuntianf/Longcell",dependencies=TRUE)Instruction
To view the documetation and tutorial of Longcell, you could visit:
https://github.com/yuntianf/Longcell/blob/main/vignettes/Longcell.ipynb
Citation
If you use Longcell for published work, please cite our manuscript:
Single cell and spatial alternative splicing analysis with long read sequencing
Yuntian Fu, Heonseok Kim, Jenea I. Adams, Susan M. Grimes, Sijia Huang, Billy T. Lau, Anuja Sathe, Paul Hess, Hanlee P. Ji, Nancy R. Zhang
bioRxiv 2023.02.23.529769; doi: https://doi.org/10.1101/2023.02.23.529769