scRNAseq-tools

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Collection of scripts for single cell RNA-seq analysis.

Environment Setup

Scripts

converter.py

Cross compatible single cell object converter for Seurat version 3.1.2, Scanpy version 1.4.4, and SingleCellExperiment (sce) version 1.8.0.

Seurat to Seurat

python3 converter.py --input_seurat <path to rds> --output_scanpy <path to h5ad>

Scanpy to Seurat

python3 converter.py --input_scanpy <path to h5ad> --output_seurat <path to rds>

Seurat to SingleCellExperiment

python3 converter.py --input_seurat <path to rds> --output_sce <path to Rdata>

SingleCellExperiment to Seurat

python3 converter.py --input_sce <path to Rdata> --output_seurat <path to rds>

SingleCellExperiment to Scanpy

python3 converer.py --input_sce <path to Rdata> --output_scanpy <path to rds>

Acknowledgments and thanks extend to the Theis and Satija laboratories for supporting interoperability between single-cell object formats.