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Welcome to scprocess documentation image title

scprocess is a snakemake pipeline for high throughput processing of single cell and single nuclei RNA sequencing data.

  • For a brief survey of the package and its capabilities, you can read the Introduction.

  • For help with installation read the Getting started section.

  • For an explanation of how to use scprocess, along with example code, how to choose parameter settings, tips and best practices, read the Usage section.

  • For a step-by-step tutorial on small example datasets, see the Tutorials section.

  • For details on input arguments see the Reference section.

  • If you get stuck, see the Troubleshooting section.

  • For how to cite scprocess, see the Citations section.