Commit History

Add instructions to convert gene annotations w/ Ensembl Biomart
77eb432

Christina Theodoris commited on

Update manuscript link to SharedIt
4f6115b

ctheodoris commited on

Update manuscript link in model card to ShareIt
dd016da

ctheodoris 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

Remove unused evalset variable from cell classification example
879a878

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

Update links including unsorted example lengths file
f0b6641

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 uniform max len for padding for predictions
67f674c

Christina Theodoris commited on

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

Christina Theodoris commited on

Update model card for 12 layer Geneformer model
0637325

ctheodoris commited on

Update model card for 12 layer Geneformer
514c5fb

ctheodoris commited on

Upload 12 layer Geneformer model
9d41e70

ctheodoris commited on

Fix bug in clearing cache
8c2fae7

Christina Theodoris commited on

Add example code for obtaining non-zero median digests
67b7f01

Christina Theodoris commited on

Update model card with license Apache 2.0
99b9a0a

ctheodoris 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

Update instructions in tokenizing example to clarify requirement for Ensembl ID
d468697

Christina Theodoris commited on

Update instructions in tokenizing example to clarify requirement for Ensembl ID
e606e1c

Christina Theodoris commited on

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

Christina Theodoris commited on

Move example input files to dataset repository to include example datasets for fine-tuning
875ef33

Christina Theodoris commited on

Update model card with information about fine-tuning
0a8c47b

ctheodoris commited on

Add example for tokenizing .loom dataset
f89f796

Christina Theodoris commited on

Update gene classification example to create directory after training arguments are defined
ebe5ee8

Christina Theodoris commited on

Subclass collator for cell classification
402ba9b

Christina Theodoris commited on

Update pretrainer for transformers==4.28.0
b925dcc

Christina Theodoris commited on

Fixes to stats and adding gene dict attempt number 2 (#13)
42e9bf9

ctheodoris commited on

Rename isp stats methods to clarify mode.
188029e

ctheodoris commited on

Reorder/sort isp stats output in vs_null mode
f4fea1e

ctheodoris commited on

Moving merged in_silico_perturber_stats.py to geneformer folder
9f2c6cc

ctheodoris commited on

Add example input labels for distinguishing bivalent promoters.
996d3e5

Christina Theodoris commited on

Add in silico perturbation example notebook.
1c2f864

Christina Theodoris commited on

Add gitignore file
ee963ba

Christina Theodoris commited on

add in silico perturbation module
d4fe544

Christina Theodoris commited on

Add example input files for gene classification of TF dosage sensitivity
0710c44

Christina Theodoris commited on

Update model card
7aebe4d

ctheodoris commited on

Update model card
8f071b7

ctheodoris commited on

add in silico perturbation module
efec1c4

Christina Theodoris commited on

Add gene name : Ensembl ID dictionary
09276dd

ctheodoris commited on

Add example for hyperparameter optimization for disease classifier
79a0c41

Christina Theodoris commited on

Update model card
b2aee1b

ctheodoris commited on

Fix bug with metadata when processing multiple .loom files (#3)
044d737

ctheodoris davidjwen commited on

Update token_dictionary.pkl
1987df4

ctheodoris commited on