Optionally use sparse tensors to encode guide x element and element x gene effects (#32)

* allow .varm element names from .uns fields

* sparse element x gene and guide x gene model

* implement sparse cis effect fitting

* add dispersion batch fx, restore base model option

* hack: default plate dim values to avoid errors

* fix hack

* more informative names for model modes

* unit test all combinations of input data

* allow reading of sparse varm fields

* remove model rendering functions

* don't fit guide effects if no elements specified

* enable full guide pooling, init gene mean -> obs

* update nb with new syntax

* clean up variable names & notebooks for prerelease

* clean up module comments

* move data subset code to reproducibility repo

* export element x gene fx summary as DataFrame

* deprecate module.get_element_effects

* clean up notebook

Author: logan-blaine

README.md

@@ -2,9 +2,9 @@
 
 # 🏎️ PerTurbo: Fast analysis of single-cell perturbation studies
 
-**PerTurbo** estimates the effects of CRISPR perturbations on single cell phenotypes using variational inference.
+**PerTurbo** is a fast statistical package for analyzing perturbation phenotypes from single cell CRISPR screens.
 
-Currently, the focus is on CRISPRi + RNA-seq (i.e. CROP-seq, Perturb-Seq) but we're planning to support other assays in the future!
+For reproducibility, see []
 
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