databio / bdshack19

Coordinating the 2019 Biomedical Data Science Hackathon at UVA
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implement Multimeasure class #6

Open gregmedlock opened 5 years ago

gregmedlock commented 5 years ago

We've started implementation of a Multimeasure class, which holds multiple AnnData objects (https://github.com/theislab/anndata). These AnnData objects are the primary object used by scanpy (https://github.com/theislab/scanpy) for analysis and visualization of single-cell RNA seq data.

jfx319 commented 5 years ago

turns out for the ingestion of data, we may not need to call scipy.sparse ourselves (may actually want to use or extend the existing scanpy/anndata for consistency):

the anndata object specs is worth a skim through, to keep this in mind. read_mtx (PS: @nsheff they implement scipy.sparse and choose the csr variant after all)

anndata implements a transpose() that also interchanges the observations/variables