Extending FastProject

FastProject is not only intended to be an analysis pipeline for single-cell RNA-seq data, but also a platform upon which different analysis techniques may be evaluated.

To this end, FastProject is extensible in a few ways.

Adding new projection methods

Since new projection methods for single-cell RNA-seq data are still being developed (see ZIFZ for example) we allow for the easy addition of new projection methods into the FastProject pipeline.

For details, see: Adding a new projection method

Adding new filter criteria

When projecting data, it is important that genes are filtered so that comparisons between cells reflect biological variation and not technical noise. We include two methods for accomplishing this in FastProject - the Hartigans Dip Test for biomodality and the use of the Fano Factor to extract high-variability genes. However, these may not be the best choice for your application. Accordingly, there is a simple method to add new filtering methods to the pipeline.

For details, see: Adding a new gene-filter scheme