Velocyto consists of two main components:
- A command line interface (CLI), that is used to run the pipeline that generates spliced/unspliced expression matrices.
- A library including functions to estimate RNA velocity from the above mentioned data matrices.
Running the CLI¶
- CLI Usage Guide
run10x- Run on 10X Chromium samples
run_smartseq2- Run on SmartSeq2 samples
run_dropest- Run on DropSeq, InDrops and other techniques
run- Run on any technique (Advanced use)
- Requirements on the input files
- About the output .loom file
- Get started with the analysis
Estimating RNA velocity¶
This guide covers the analysis and assumes that you have produced a .loom file using the velocyto CLI (follow the guide above).