Data Type Requirements

Data type requirements

Hooke is built for experiments with multiple treatments and replicates, taking advantage of replicates in various groups or perturbations. As input, Hooke takes in a cell x gene matrix where cells are annotated according to type (or cluster) and by which sample or specimen they came from. It will aggregate cells according to type and by sample. This collapses the matrix into a new, smaller matrix where rows are cell types and the columns denote how many cells of that type were present in each sample. We refer to this as a cell type abundance matrix.

Using a Monocle3 object

Hooke extends the cell data count set. A Monocle3 object can be directly plugged into Hooke.

Using a Seurat object

Currently Hooke only supports Monocle3 cell data set objects. If using Seurat, please see the Seurat documentation on how to convert a Seurat object to a Monocle3 object.