scHPTM benchmark

This repository contains the code for benchmarking the quality of the representation of single-cell histone post translational modifications (scHPTM).

We evaluate the effect of the following factors:

• Matrix construction.
• Quality control (based on coverage).
• Feature selection effect (using HVG or coverage).
• Role of number of cells per experiment (by downsampling).
• Role of coverage per cell (by downsampling cells based on coverage).
• Role of normalization used (RPM or TF-IDF).
• Role of dimension reduction algorithm (using 7 standard single-cell epigenetics pipelines).

The evaluation relies on having a robust co-assay (either transcriptomic or surface proteins), and measuring how well the scHPTM representation conserves the local geometry that can be observed in the reference co-assay.