Software

Contrastive PCA - A generalization of PCA that discovers important features/directions that are enriched in one dataset relative to another. Applications: discovering subgroups in RNA-Seq data, de-noising images on complex backgrounds, visualizing ancestry trends based on SNPs, feature identification and selection.
Paper - Github Code - Python library

SPROUT - A machine learning tool to predict the DNA repair outcome in CRISPR-cas9 knockout experiments. The software predicts various summary statistics of the DNA repair outcome as a result of a double stranded CRISPR-cas9 cut including, fraction of cells with an insertion/deletion, average insertion/deletion length, diversity, most probable inserted nucleotide given a single base pair insertion.
Paper - Github Code - Website