Geneformer / geneformer

Commit History

Add option for variable input_size and to add CLS/SEP Tokens (#299)
aa25cd2
verified

ctheodoris hchen725 commited on

add load model for train and fix validate anchor gene error
0d675a3

Christina Theodoris commited on

Handle case of single gene del for isp modeling of gene embs
316d817

Christina Theodoris commited on

edit docstring format to highlight options
e3330a6

Christina Theodoris commited on

edit docstring codeblock highlighting
d1931b1

Christina Theodoris commited on

update type of null_dict_list in docstring
79788b6

Christina Theodoris commited on

change doc formatting
17f036a

Christina Theodoris commited on

add sphinx docs
2a0dcbe

Christina Theodoris commited on

update dependencies, reinstate compatibility with python<3.9 with typing for List
10d3f10

Christina Theodoris commited on

Add option for modified batch size for loom tokenizer
0960cf6

Christina Theodoris commited on

Add functions for extracting gene embeddings, move state_embs_dict outside isp, fix bugs in isp
2f25aea

Christina Theodoris commited on

Add option for modifying chunk size for anndata tokenizer
fd93ebf

Christina Theodoris commited on

Add option to output embs as tensor
624349c

Christina Theodoris commited on

Add memory-efficient method for computing emb summary statistics
6caf480

Christina Theodoris commited on

Fixed bug with the double removing of indices when cell_states_to_model is false (#188)
0adfe67

ctheodoris davidjwen commited on

Added feature to perturb a set of indices to help with debugging and with very large runtimes (#175)
f115e8f

ctheodoris davidjwen commited on

Re-update stats to handle case of empty alt_states
78517d8

Christina Theodoris commited on

Add handling for case of alt_states being empty list
9e8dbe5

Christina Theodoris commited on

Remove print statement from PR
c4b1f94

ctheodoris commited on

Fixed error with perturbing individual genes and updated ways to specify cell_states_to_model (#146)
9169bfd

ctheodoris davidjwen commited on

Add error message for "gene" embedding extraction under development.
65b4915

Christina Theodoris commited on

Rename heatmap legend to be correct label
badcca6

Christina Theodoris commited on

Add function to extract and plot cell embeddings
d154fee

Christina Theodoris commited on

Add error for no files found and suppress loompy import warning
abdf980

Christina Theodoris commited on

Add sorting for aggregating data for goal state shifts
50e921d

Christina Theodoris commited on

Fix min_genes to be >= tokens to perturb as a group
268e566

Christina Theodoris commited on

Update tokenizer to allow tokenization without custom cell attributes
57b9778

Christina Theodoris commited on

Update isp to allow modeling single perturbation in multiple cells as batches
acd253c

Christina Theodoris commited on

Update internal format of anchor token to list for consistency with genes to perturb
b36d210

Christina Theodoris commited on

Add filtering for start state cells prior to in silico perturbation when modeling cell states
bb217cf

Christina Theodoris commited on

Correct order of state dict in in silico perturber stats and tensor dims of alt state emb in in silico perturber
3d06203

Christina Theodoris commited on

Add explanation of output columns and sort by largest shift
3072225

Christina Theodoris commited on

Modify tokenizer to allow renaming attr names btwn loom and .dataset
e78c44d

Christina Theodoris commited on

Modify quant_layers to convert layer nums to integers before calculating max
2181aa4

Christina Theodoris commited on

Modify documentation for modeling only 2 cell states
019165f

Christina Theodoris commited on

Add instructions for modeling only 2 states and modify stats script for that option
912860d

Christina Theodoris commited on

Add function to create remainder emb for in silico overexpression batch
feeecd0

Christina Theodoris commited on

Add mixture model option for gene-gene interaction stats
dc1481d

Christina Theodoris commited on

Add stats with mixture model to determine whether test perturbation is in impact component
d20ad0a

Christina Theodoris commited on

Fix bug in clearing cache
8c2fae7

Christina Theodoris commited on

Fix filter_data to allow value of None for no filtering
5fcf2b8

Christina Theodoris commited on

Add further explanation regarding input file format for transcriptome tokenizer
c34ead6

Christina Theodoris commited on

Add further explanation to tokenizer example script and updated tokenizer to match loompy raised error
78dd83b

Christina Theodoris commited on