SCherlock is a set of utilities to make the most out of your single-cell data. It is supposed to be used in conjuntion with anndata and scanpy.
The main features of SCherlock are all related to detailed qualitative and quantitative analysis of reads - are there are changes in isoforms, promoters or enhancers? It supports a new file format, CellPile, which enables quick pile-up generation for each clustering you perform. It can also take output from Isocounter, a more versatile feature counter.