scanpy-scripts

A command-line interface for functions of the Scanpy suite, to facilitate flexible constrution of workflows, for example in Galaxy, Nextflow, Snakemake etc.

Install

The recommended way of using this package is through the latest container produced by Bioconda here. If you must, one can install scanpy-scripts via conda:

conda install scanpy-scripts

pip installation is also possible, however the version of mnnpy is not patched as in the conda version, and so the integrate command will not work.

pip install scanpy-scripts

For development installation, we suggest following the github actions python-package.yml file.

Currently, tests run on python 3.9, so those are the recommended versions if not installing via conda. BKNN doesn't currently install on Python 3.10 due to a skip in Bioconda.

Test installation

There is an example script included:

scanpy-scripts-tests.bats

This requires the bats testing framework to run. The script downloads a well-known test 10X dataset and executes all of the commands described below.

Commands

Available commands are described below. Each has usage instructions available via --help, consult function documentation in scanpy for further details.

Usage: scanpy-cli [OPTIONS] COMMAND [ARGS]...

  Command line interface to [scanpy](https://github.com/theislab/scanpy)

Options:
  --debug              Print debug information
  --verbosity INTEGER  Set scanpy verbosity
  --version            Show the version and exit.
  --help               Show this message and exit.

Commands:
  read       Read 10x data and save in specified format.
  filter     Filter data based on specified conditions.
  norm       Normalise data per cell.
  hvg        Find highly variable genes.
  scale      Scale data per gene.
  regress    Regress-out observation variables.
  pca        Dimensionality reduction by PCA.
  neighbor   Compute a neighbourhood graph of observations.
  embed      Embed cells into two-dimensional space.
  cluster    Cluster cells into sub-populations.
  diffexp    Find markers for each clusters.
  paga       Trajectory inference by abstract graph analysis.
  dpt        Calculate diffusion pseudotime relative to the root cells.
  integrate  Integrate cells from different experimental batches.
  multiplet  Execute methods for multiplet removal.
  plot       Visualise data.

Versioning

Major and major versions will follow the scanpy versions. The first digit of the patch should follow the scanpy patch version as well, subsequent digits in the patch are reserved for changes in this repository.