Fixed bugs related to overexpressing genes

Fixed bug with the double removing of indices when cell_states_to_model is false (#188)

Upload in_silico_perturber.py (#187)

Added feature to perturb a set of indices to help with debugging and with very large runtimes (#175)

Re-update stats to handle case of empty alt_states

Add handling for case of alt_states being empty list

Remove print statement from PR

Fixed bug in gen_attention_mask with len > max_len (#158)

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

Add error message for "gene" embedding extraction under development.

Rename heatmap legend to be correct label

Add function to extract and plot cell embeddings

Add error for no files found and suppress loompy import warning

Add sorting for aggregating data for goal state shifts

Fix min_genes to be >= tokens to perturb as a group

Update tokenizer to allow tokenization without custom cell attributes

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

Update internal format of anchor token to list for consistency with genes to perturb

Add filtering for start state cells prior to in silico perturbation when modeling cell states

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 tokenizer to allow renaming attr names btwn loom and .dataset

Modify quant_layers to convert layer nums to integers before calculating max

Modify documentation for modeling only 2 cell states

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

Add function to create remainder emb for in silico overexpression batch

Add mixture model option for gene-gene interaction stats

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

Fix bug in clearing cache

Fix filter_data to allow value of None for no filtering

Add further explanation regarding input file format for transcriptome tokenizer

Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error

Subclass collator for cell classification

Update pretrainer for transformers==4.28.0

Upload gene_name_id_dict.pkl (#14)

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

add in silico perturbation module

Add gene name : Ensembl ID dictionary

Fix bug with metadata when processing multiple .loom files (#3)

Update token_dictionary.pkl

Delete geneformer/token_dictionary.pkl

Add data collator for gene classification and example for gene classification

Add data collator for cell classification and example for cell classification

Add Geneformer trainer and pretraining example

Add Geneformer tokenizer and updated model card