scArchest
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scArches (PyTorch) - single-cell architecture surgery
Installation
API
How to share your models?
Model database
A few tips on training models
Examples
Unsupervised surgery pipeline with SCVI
Semi-supervised surgery pipeline with SCANVI
Multi-Modal Surgery Pipeline with TOTALVI
Unsupervised surgery pipeline with TRVAE
scArchest
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C
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D
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G
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H
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L
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M
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P
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R
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S
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U
C
create_deposition() (in module scarchest.zenodo.deposition)
D
delete_deposition() (in module scarchest.zenodo.deposition)
differential_expression() (scarchest.models.TOTALVI method)
download_file() (in module scarchest.zenodo.file)
download_model() (in module scarchest.zenodo)
G
get_all_deposition_ids() (in module scarchest.zenodo.deposition)
get_asw() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_classification_accuracy() (scarchest.plotting.SCVI_EVAL method)
get_ebm() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_f1_score() (scarchest.plotting.SCVI_EVAL method)
get_feature_correlation_matrix() (scarchest.models.TOTALVI method)
get_knn_purity() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_latent() (scarchest.models.TRVAE method)
get_latent_library_size() (scarchest.models.TOTALVI method)
get_latent_representation() (scarchest.models.TOTALVI method)
get_latent_score() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_likelihood_parameters() (scarchest.models.TOTALVI method)
get_model_arch() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_nmi() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
get_normalized_expression() (scarchest.models.TOTALVI method)
get_protein_foreground_probability() (scarchest.models.TOTALVI method)
get_reconstruction_error() (scarchest.models.TOTALVI method)
H
history() (scarchest.models.SCANVI property)
L
label_encoder() (in module scarchest.dataset)
latent_as_anndata() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
load_query_data() (scarchest.models.TRVAE class method)
M
module
scarchest.dataset
scarchest.plotting
scarchest.zenodo
scarchest.zenodo.deposition
scarchest.zenodo.file
P
plot_history() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
plot_latent() (scarchest.plotting.SCVI_EVAL method)
(scarchest.plotting.TRVAE_EVAL method)
posterior_predictive_sample() (scarchest.models.TOTALVI method)
predict() (scarchest.models.SCANVI method)
publish_deposition() (in module scarchest.zenodo.deposition)
R
remove_sparsity() (in module scarchest.dataset)
S
sankey_diagram() (in module scarchest.plotting)
SCANVI (class in scarchest.models)
scarchest.dataset
module
scarchest.plotting
module
scarchest.zenodo
module
scarchest.zenodo.deposition
module
scarchest.zenodo.file
module
SCVI (class in scarchest.models)
SCVI_EVAL (class in scarchest.plotting)
setup_anndata() (in module scarchest.dataset)
T
TOTALVI (class in scarchest.models)
train() (scarchest.models.SCANVI method)
(scarchest.models.TOTALVI method)
(scarchest.models.TRVAE method)
TRVAE (class in scarchest.models)
TRVAE_EVAL (class in scarchest.plotting)
trVAEDataset (in module scarchest.dataset)
U
update_deposition() (in module scarchest.zenodo.deposition)
upload_file() (in module scarchest.zenodo.file)
upload_model() (in module scarchest.zenodo)
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