Geneformer / geneformer

Commit History

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

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

add in silico perturbation module
d4fe544

Christina Theodoris commited on

add in silico perturbation module
efec1c4

Christina Theodoris commited on

Add gene name : Ensembl ID dictionary
09276dd

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

Delete geneformer/token_dictionary.pkl
870b99b

ctheodoris commited on

Add data collator for gene classification and example for gene classification
edacd12

Christina Theodoris commited on

Add data collator for cell classification and example for cell classification
088ea6e

Christina Theodoris commited on

Add Geneformer trainer and pretraining example
bcc03e8

Christina Theodoris commited on

Add Geneformer tokenizer and updated model card
5426788

Christina Theodoris commited on