What’s included
This is the public release of SCALPEL, a modular Nextflow-based pipeline for quantifying transcript isoform expression and alternative polyadenylation (APA) using 3'-tagged single-cell RNA-seq data.
Highlights
- Full support for 10X Genomics and DropSeq datasets
- Isoform-aware quantification from filtered reads
- Internal priming correction using custom annotation
- APA-aware DGE matrix and Seurat-compatible
.RDSoutput - Differential Isoform Usage (DIU) analysis between clusters or conditions
- Conda-based and Apptainer-based deployment options
- Fully documented on the Wiki