cellHarmony

cellHarmony is a computational tool for analyzing and comparing cell populations from single-cell RNA-Seq datasets. It enables the identification of normal and diseased transcriptional cell populations. It uses an unsupervised approach to match single-cell transcriptomes and compute differences in cell-type-specific gene expression across multiple cell populations.

Key features of cellHarmony include:

1. Community-clustering and alignment strategy to efficiently and accurately match single-cell transcriptomes.

2. Automatic identification of distinct and shared gene programs among cell types.

3. Identification of impacted pathways and transcriptional regulatory networks to understand the effects of perturbations at a systems level.

4. Implementation as a Python package and integrated workflow within the AltAnalyze software.