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.
Release files for scanpy-scripts 1.9.301
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Source distribution (sdist)
| File | Size | Uploaded | |
|---|---|---|---|
| scanpy-scripts-1.9.301.tar.gz | 47.5 kB | Details |
Built distribution (wheel)
| File | Interpreter | ABI | Platform | Reset |
|---|---|---|---|---|
| scanpy_scripts-1.9.301-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 102.6 kB
Release files / scanpy-scripts-1.9.301.tar.gz
| Download URL | scanpy-scripts-1.9.301.tar.gz |
|---|---|
| Size | 47.5 kB |
| Tags | Source |
|
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Release files / scanpy_scripts-1.9.301-py3-none-any.whl
| Download URL | scanpy_scripts-1.9.301-py3-none-any.whl |
|---|---|
| Size | 55.1 kB |
| Tags | Python 3 |
|
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