move dicts to init

update perturber stats to reflect cos sim and emb_extractor to suppress warnings for non-cls

update to account for set of perturbed genes with aggregate_data

Upload in_silico_perturber_stats.py (#313)

Add classifier module and examples

Handle case of single gene del for isp modeling of gene embs

edit docstring codeblock highlighting

update type of null_dict_list in docstring

change doc formatting

add sphinx docs

Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp

Add option to output embs as tensor

Re-update stats to handle case of empty alt_states

Add handling for case of alt_states being empty list

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)

Add sorting for aggregating data for goal state shifts

Update isp to allow modeling single perturbation in multiple cells as batches

Correct order of state dict in in silico perturber stats and tensor dims of alt state emb in in silico perturber

Add explanation of output columns and sort by largest shift

Modify documentation for modeling only 2 cell states

Add instructions for modeling only 2 states and modify stats script for that option

Add mixture model option for gene-gene interaction stats

Add stats with mixture model to determine whether test perturbation is in impact component

Fixes to stats and adding gene dict attempt number 2 (#13)

Rename isp stats methods to clarify mode.

Reorder/sort isp stats output in vs_null mode

add in silico perturbation module