Welcome to CellBender’s documentation!


CellBender is a software package for eliminating technical artifacts from high-throughput single-cell RNA sequencing (scRNA-seq) data.

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

For an explanation of when and how and why to use CellBender in your analysis pipeline, along with example code, how to choose parameter settings, and tips on quality control, read the Usage section.

For a step-by-step tutorial on a simplified example dataset, see the Quick start tutorial section.

For details on input arguments and the output file format, see the Reference section.

For troubleshooting and an FAQ, see the Troubleshooting section.