GIFTwrap

This package provides tools for dealing with GIFT-seq data. The giftwrap package is designed for both processing of GIFT-seq raw data and provides tools for downstream analysis of GIFT-seq data.

Main Features

• Data Processing: Tools for processing GIFT-seq-based FastQ files into counts matrices.
• Basic QC: Automatic quality control of GIFT-seq data based on 10X Cell Ranger cell calls on the paired transcriptomes.
• Downstream Analysis: Functions for filtering and analyzing GIFT-seq data, including single-cell genotyping and imputation.
• Spatial Analysis: Tools for spatial analysis of GIFT-seq data, including visualization and spatial clustering.

Installation

Please refer to our installation guide for detailed instructions on how to install the giftwrap package.

Usage

Please review our tutorials and examples to get started with using the giftwrap package for your GIFT-seq data analysis.

• Getting Started
• Processing GIFT-seq Data
• Analyzing GIFT-seq Data
• Imputing Genotypes
• Spatial Analysis
• Seurat Integration
• Extending GIFTwrap

Contributing

We welcome contributions to the giftwrap package! Please see our contributing guide for more information on how to contribute to the project.

Additional Information

For more information on GIFT-seq, please refer to our publication: ...