SPADA

Code for SPADA lab genomics research on bulk and single-cell RNA-sequencing data.

The Python folder contains code which implements

1. a joint bulk and scRNA-seq data simulation based on the URSM (https://projecteuclid.org/euclid.aoas/1520564486) and ZIFA (https://genomebiology.biomedcentral.com/articles/10.1186/s13059-015-0805-z) models
2. a hypothesis test for whether a bulk and single-cell dataset are joint (come from similar tissue)
3. a new algorithm called cluster heterogeneity for measuring the similarity of clustered datasets.
4. Implementations of the sparse subspaces and k-subspaces clustering algorithms. A big thank you to Abhinav Garg for his SSC code at https://github.com/abhinav4192/sparse-subspace-clustering-python.

The Cpp folder contains code for preprocessing datasets stored in csv and tsv files.