Welcome to velocyto.py!

Velocyto is a library for the analysis of RNA velocity.

Velocyto includes a command line tool and an analysis pipeline

Warning

CLI API has been improved and differs from previous versions. Please refer to the updated CLI tutorial and API session to know more about the changes.

Warning

velocyto-team is about to release velocyto.py v1.0 in the meanwhile API will be subject to minor changes until 1.0 release.

Note

Please do not hesitate to report issues on our Github page. We try to respond within the few hours to all the users.

Contents

• Installation Guide
  • Requirements
  • Install using PyPI
  • Install from source
  • Install using conda
  • Extra requirements

• Tutorial
  • Getting Started
  • Running the CLI
    • CLI Usage Guide
      • Introduction
      • Preparation
        • Download genome annotation file
        • Download expressed repeats annotation
      • Running velocyto
      • 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)
        • Notes on first runtime and parallelization
        • Run with different logics
      • Requirements on the input files
      • About the output .loom file
        • Merging multiple samples/lanes in a single file
      • Get started with the analysis
  • Estimating RNA velocity
    • Analysis Pipeline
      • Velocyto Loom
      • Start a new analysis - Preliminary Filtering
      • Preparation for gamma fit
      • Gamma fit and extrapolation
      • Projection of velocity onto embeddings

• API
  • Command Line API
    • CLI Usage
      • Command Line Tool API
        • velocyto
          • run
          • run-dropest
          • run-smartseq2
          • run10x
          • tools
            • dropest-bc-correct
  • Library API
    • The Analysis module
      • velocyto.analysis module
    • The Estimation module
      • velocyto.estimation module
    • The Neighbors module
      • velocyto.neighbors module
    • The Diffusion module
      • velocyto.diffusion module
    • The Serialization module
      • velocyto.serialization module
  • Internals
    • CLI Internals
      • velocyto.counter module
      • velocyto.transcript_model module
      • velocyto.segment_match module
      • velocyto.feature module
      • velocyto.indexes module
      • velocyto.molitem module
      • velocyto.gene_info module
      • velocyto.read module
  • Customizable Internals
    • CLI Logic
      • velocyto.logic module

• Notebooks

• Changelog

• License

• Authors and citations
  • Cite velocyto
  • Note on the authors of velocyto

Indices and tables

• Index
• Module Index
• Search Page