Scripts for using scanpy from the command line
A command-line interface for functions of the Scanpy suite, to facilitate flexible constrution of workflows, for example in Galaxy, Nextflow, Snakemake etc.
conda install scanpy-scripts # or pip3 install scanpy-scripts
There is an example script included:
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. plot Visualise data.
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