Longcell

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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://yuntianf.github.io/Longcell/

Citation

If you use Longcell for published work, please cite our manuscript:

Fu Y, Kim H, Roy S, et al. Single cell and spatial alternative splicing analysis with Nanopore long read sequencing[J]. Nature Communications, 2025, 16(1): 6654.