Instructions to use ctheodoris/Geneformer with libraries, inference providers, notebooks, and local apps. Follow these links to get started.
- Libraries
- Transformers
How to use ctheodoris/Geneformer with Transformers:
# Use a pipeline as a high-level helper from transformers import pipeline pipe = pipeline("fill-mask", model="ctheodoris/Geneformer")# Load model directly from transformers import AutoTokenizer, AutoModelForMaskedLM tokenizer = AutoTokenizer.from_pretrained("ctheodoris/Geneformer") model = AutoModelForMaskedLM.from_pretrained("ctheodoris/Geneformer", device_map="auto") - Inference
- Notebooks
- Google Colab
- Kaggle
File size: 622 Bytes
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=========================
.. automodule:: geneformer.emb_extractor
:members:
:undoc-members:
:show-inheritance:
:exclude-members:
accumulate_tdigests,
gen_heatmap_class_colors,
gen_heatmap_class_dict,
get_embs,
label_cell_embs,
label_gene_embs,
make_colorbar,
plot_heatmap,
plot_umap,
summarize_gene_embs,
tdigest_mean,
tdigest_median,
test_emb,
update_tdigest_dict,
update_tdigest_dict_mean,
update_tdigest_dict_median,
valid_option_dict,
validate_options
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