Package Overview | Guided Walk-Through | Installation | Prerequisites | Input Files | Step-by-Step Guide | Step-1 | The Help Page for the determine_split_regions() Function | Check formatting of input files and build BED-like split intervals | Step-2 | The Help Page for the process_gtf() Function | Generate Gene Annotation (GTF) File in Compatible to Cell Ranger ARC Format | Step-3 | Step-4 | Prepare config File | Run Cell Ranger ARC | Citation | License | Contributing | Acknowledgements

1. Purpose | 2. {scShardSplitRef} Guided Walkthrough Using a Toy Example | Installation | Prerequisites | Input Files | Workflow | 1. Determine Split Regions | The Help Page for determine_split_regions() | Usage Example: determine_split_regions() | Algorithm Explanation: How determine_split_regions() works | No Overlap with Gene Coordinates | Overlap with Gene Coordinates | 2. Process a GTF file by assigning split-region sequence names | The Help Page for process_gtf() | Usage Example: process_gtf() | 3. Acknowledgements