Single-Cell RNA Seq Example (#265)

* data processing code

* model doesnt compile yet

* fixed dimensions but module naming issue

* before switching to interaction version of model

* presentation w/ alvin

* cleaned up summary stats section and focus on one drug

* before switching to multiworld for ate

* eli shape corrections

* uncomitted changes w/ eli re. shapes

* eli's fix of counterfactual

* clean up

* rewording

* change of notation and reran notebook

* removed old sentence

* fixed typo

* removed some masking and redundancy

* made dropout a function of confounders too

* Ra aq scrna (#263)

* Add an effect handler for inserting factor statements (#238)

* Add a Factors handler for inserting new factors

* docs and test

* lint

* Add a BiasedPreemptions handler (#239)

* Add BiasedPreemptions handler

* test and tiny refactoring

* updated copywrite (#254)

* pin sphinx version to 7.1.2 to fix docs building (#256)

* pin sphinx version to 7.1.2 fixes doc building locally

* remove pypandoc

* Update requirements.txt

* Update setup.py

* pin sphinx_rtd_theme==1.3.0 to fix docs deployment (#262)

* 1. add preprocessing method for expression normalization
2. test more HDAC drugs
3. reproduce raj results

* add pseudobulk comparison

* add T>0 for theta_drug; clean up notebook for one drug with high IC50

* change T>0 to T for theta_drug; did a bunch of experiments for library size, not improved yet

* use corrected gene expression for ate estimation

* replace the likelihood to Poisson; it seems working for HDACi

---------

Co-authored-by: eb8680 <[email protected]>
Co-authored-by: Sam Witty <[email protected]>

* cleaned up notebook and fixed some bugs

* fixed some bugs and cleaned up references and some notation

* fixed drug typo and removed treatment mask

* query models, add latent factor per cell

* removed old file, did not finish running on all genes so moving to gcp

* cleaned up some more text

* target genes specified, kernel crashes on last fig

* fixed missing ref

* reducted num samples to fix memory issue

* fixed typo

* updated target genes w/ chip targets and fixed plotting bug

* added alvins descriptions + some rewriting

* fixed some typos

* added pca discussion

* forgot to save when committing

* fixed typo

---------

Co-authored-by: Raj Agrawal <[email protected]>
Co-authored-by: Alvin Qin <[email protected]>
Co-authored-by: eb8680 <[email protected]>
Co-authored-by: Sam Witty <[email protected]>