Geneformer / geneformer

11.5 MB

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20 contributors

History: 162 commits

ctheodoris

ensure anndata/zarr returns data rather than dir if not collapse_gene_ids

0efc3b3 verified 7 months ago

gene_dictionaries_30m
Update geneformer/tokenizer.py (#415) over 1 year ago
mtl
move import wandb to conditional 11 months ago
__init__.py

1.65 kB
update with V2 models 10 months ago
classifier.py

66.6 kB
move V1 autoformatting to after validate_options 10 months ago
classifier_utils.py

23.6 kB
add option for relabeling data from prior label class dict, update dict paths in manifest 10 months ago
collator_for_classification.py

31.7 kB
silence tensor copy warning 10 months ago
emb_extractor.py

33.3 kB
plot umap for all labels in same view 10 months ago
ensembl_mapping_dict_gc104M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
3.96 MB
xet

add V2 models 10 months ago
evaluation_utils.py

10.1 kB
Update geneformer/evaluation_utils.py to be compatible with different versions of the datasets package. (#552) 9 months ago
gene_median_dictionary_gc104M.pkl
Detected Pickle imports (2)
- "numpy.dtype",
- "numpy.core.multiarray.scalar"
How to fix it?
1.51 MB
xet

add V2 models 10 months ago
gene_name_id_dict_gc104M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
1.66 MB
xet

add V2 models 10 months ago
in_silico_perturber.py

67.5 kB
update V1 token dict usage to self attr 10 months ago
in_silico_perturber_stats.py

45.7 kB
update with V2 models 10 months ago
mtl_classifier.py

14.5 kB
fully qualified imports to resolve name-space conflicts (#532) 11 months ago
perturber_utils.py

32.3 kB
Update geneformer/perturber_utils.py to be compatible with different versions of the datasets package. (#553) 9 months ago
pretrainer.py

29.5 kB
remove unused imports while no longer using distributed sampler over 1 year ago
token_dictionary_gc104M.pkl
Pickle imports
- No problematic imports detected
What is a pickle import?
426 kB
xet

add V2 models 10 months ago
tokenizer.py

34.6 kB
ensure anndata/zarr returns data rather than dir if not collapse_gene_ids 7 months ago

Pickle imports

Detected Pickle imports (2)

Pickle imports

Pickle imports