scDALI

scDALI maps cell-state-specific allelic imbalance by integrating allele-specific quantifications with single-cell sequencing-derived cellular state information to characterize genetic regulation across heterogeneous cell populations.

Key Features:

• Allele-Specific Analysis: Performs allele-specific analyses on single-cell data to detect and characterize differential allelic imbalance specific to particular cell states.
• Integration of Cellular State Information: Combines cellular state information with allelic quantifications from single-cell sequencing datasets to link genetic effects to cell types, developmental stages, or lineages.
• Versatility Across Data Types: Applicable to multiple single-cell sequencing technologies, including single-cell ATAC-seq (scATAC-seq) and single-cell RNA-seq (scRNA-seq).

Scientific Applications:

• Developmental Biology: Applied to scATAC-seq profiles from developing F1 Drosophila embryos to uncover genetic effects specific to developmental stages or lineages.
• Stem Cell Research: Used with differentiating human induced pluripotent stem cells (iPSCs) to identify heterogeneous genetic effects across cell types and differentiation pathways.

Methodology:

Implements a statistical model that integrates allelic quantifications from single-cell sequencing with cellular state information to detect and characterize differential allelic imbalance.