scGPT
latest
Getting Started:
Introduction
installation
Tutorials:
GRN Inference on Pre-trained Model
Fine-tuning on Pre-trained Model with Batch Integration
Fine-tuning on Pre-trained Model for Cell-type Annotation
Fine-tuning Pre-trained Model for Perturbation Prediction
Reference Mapping Using cell embedding by pretrained scGPT model
API Reference:
scgpt package
References:
FAQ
References
scGPT
Index
Edit on GitHub
Index
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B
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C
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D
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E
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F
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G
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H
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I
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K
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M
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N
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P
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R
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U
A
add_file_handler() (in module scgpt.utils.util)
AdversarialDiscriminator (class in scgpt.model.model)
append_study() (scgpt.scbank.databank.DataBank method)
average_vector_results() (scgpt.tasks.grn.GeneEmbedding static method)
B
backward() (scgpt.model.grad_reverse.GradReverse static method)
batch_from_anndata() (scgpt.scbank.databank.DataBank class method)
BatchLabelEncoder (class in scgpt.model.model)
binning() (in module scgpt.preprocess)
bn_handle (scgpt.model.dsbn.DomainSpecificBatchNorm1d property)
(scgpt.model.dsbn.DomainSpecificBatchNorm2d property)
build_fast_transformer_encoder() (scgpt.model.model.FastTransformerEncoderWrapper static method)
build_length_mask() (scgpt.model.model.FastTransformerEncoderWrapper static method)
C
category_str2int() (in module scgpt.utils.util)
CategoryValueEncoder (class in scgpt.model.model)
cell_ids (scgpt.scbank.data.MetaInfo attribute)
check_logged() (scgpt.preprocess.Preprocessor method)
ClsDecoder (class in scgpt.model.generation_model)
(class in scgpt.model.model)
cluster_definitions_as_df() (scgpt.tasks.grn.GeneEmbedding method)
compute_similarities() (scgpt.tasks.grn.GeneEmbedding method)
ContinuousValueEncoder (class in scgpt.model.model)
criterion_neg_log_bernoulli() (in module scgpt.loss)
custom_filter() (scgpt.scbank.databank.DataBank method)
D
data (scgpt.scbank.data.DataTable attribute)
data_tables (scgpt.scbank.databank.DataBank attribute)
DataBank (class in scgpt.scbank.databank)
DataCollator (class in scgpt.data_collator)
DataTable (class in scgpt.scbank.data)
define_wandb_metrcis() (in module scgpt.trainer)
delete_study() (scgpt.scbank.databank.DataBank method)
do_binning (scgpt.data_collator.DataCollator attribute)
do_mlm (scgpt.data_collator.DataCollator attribute)
do_padding (scgpt.data_collator.DataCollator attribute)
DomainSpecificBatchNorm1d (class in scgpt.model.dsbn)
DomainSpecificBatchNorm2d (class in scgpt.model.dsbn)
E
embed_data() (in module scgpt.tasks.cell_emb)
encode_batch() (scgpt.model.generation_model.TransformerGenerator method)
(scgpt.model.model.TransformerModel method)
eval_scib_metrics() (in module scgpt.utils.util)
eval_testdata() (in module scgpt.trainer)
evaluate() (in module scgpt.trainer)
ExprDecoder (class in scgpt.model.model)
F
FastTransformerEncoderWrapper (class in scgpt.model.model)
filter() (scgpt.scbank.databank.DataBank method)
find_required_colums() (in module scgpt.utils.util)
FlashTransformerEncoderLayer (class in scgpt.model.model)
forward() (scgpt.model.generation_model.ClsDecoder method)
(scgpt.model.generation_model.GeneEncoder method)
(scgpt.model.generation_model.PositionalEncoding method)
(scgpt.model.generation_model.Similarity method)
(scgpt.model.generation_model.TransformerGenerator method)
(scgpt.model.grad_reverse.GradReverse static method)
(scgpt.model.model.AdversarialDiscriminator method)
(scgpt.model.model.BatchLabelEncoder method)
(scgpt.model.model.CategoryValueEncoder method)
(scgpt.model.model.ClsDecoder method)
(scgpt.model.model.ContinuousValueEncoder method)
(scgpt.model.model.ExprDecoder method)
(scgpt.model.model.FastTransformerEncoderWrapper method)
(scgpt.model.model.FlashTransformerEncoderLayer method)
(scgpt.model.model.GeneEncoder method)
(scgpt.model.model.MVCDecoder method)
(scgpt.model.model.PositionalEncoding method)
(scgpt.model.model.Similarity method)
(scgpt.model.model.TransformerModel method)
from_anndata() (scgpt.scbank.databank.DataBank class method)
from_dict() (scgpt.tokenizer.gene_tokenizer.GeneVocab class method)
from_file() (scgpt.tokenizer.gene_tokenizer.GeneVocab class method)
from_path() (scgpt.scbank.data.MetaInfo class method)
(scgpt.scbank.databank.DataBank class method)
G
gene_vocab (scgpt.scbank.databank.DataBank property)
gene_vocab_md5 (scgpt.scbank.data.MetaInfo attribute)
gene_vocabulary() (in module scgpt.utils.util)
GeneEmbedding (class in scgpt.tasks.grn)
GeneEncoder (class in scgpt.model.generation_model)
(class in scgpt.model.model)
generate() (scgpt.model.model.TransformerModel method)
generate_network() (scgpt.tasks.grn.GeneEmbedding method)
generate_square_subsequent_mask() (in module scgpt.model.generation_model)
(in module scgpt.model.model)
generate_vector() (scgpt.tasks.grn.GeneEmbedding method)
generate_weighted_vector() (scgpt.tasks.grn.GeneEmbedding method)
GeneVocab (class in scgpt.tokenizer.gene_tokenizer)
get_adata() (scgpt.tasks.grn.GeneEmbedding method)
get_batch_cell_embeddings() (in module scgpt.tasks.cell_emb)
get_default_gene_vocab() (in module scgpt.tokenizer.gene_tokenizer)
get_free_gpu() (in module scgpt.utils.util)
get_git_commit() (in module scgpt.utils.util)
get_metagenes() (scgpt.tasks.grn.GeneEmbedding method)
get_similar_genes() (scgpt.tasks.grn.GeneEmbedding method)
grad_reverse() (in module scgpt.model.grad_reverse)
GradReverse (class in scgpt.model.grad_reverse)
H
histogram() (in module scgpt.utils.util)
I
immediate_save (scgpt.scbank.setting.Setting attribute)
init_weights() (scgpt.model.generation_model.TransformerGenerator method)
(scgpt.model.model.TransformerModel method)
is_loaded (scgpt.scbank.data.DataTable property)
isnotebook() (in module scgpt.utils.util)
K
keep_first_n_tokens (scgpt.data_collator.DataCollator attribute)
L
link() (scgpt.scbank.databank.DataBank method)
load() (scgpt.scbank.data.MetaInfo method)
(scgpt.scbank.databank.DataBank method)
load_all() (scgpt.scbank.databank.DataBank method)
load_anndata() (scgpt.scbank.databank.DataBank method)
load_pretrained() (in module scgpt.utils.util)
load_table() (scgpt.scbank.databank.DataBank method)
M
main_data (scgpt.scbank.databank.DataBank property)
main_process_only() (in module scgpt.utils.util)
main_table_key (scgpt.scbank.data.MetaInfo attribute)
(scgpt.scbank.databank.DataBank property)
MainProcessOnly (class in scgpt.utils.util)
map_raw_id_to_vocab_id() (in module scgpt.utils.util)
mask_value (scgpt.data_collator.DataCollator attribute)
masked_mse_loss() (in module scgpt.loss)
masked_relative_error() (in module scgpt.loss)
max_length (scgpt.data_collator.DataCollator attribute)
max_tokenize_batch_size (scgpt.scbank.setting.Setting attribute)
meta_info (scgpt.scbank.databank.DataBank attribute)
MetaInfo (class in scgpt.scbank.data)
mlm_probability (scgpt.data_collator.DataCollator attribute)
module
scgpt.data_collator
scgpt.data_sampler
scgpt.loss
scgpt.model
scgpt.model.dsbn
scgpt.model.generation_model
scgpt.model.grad_reverse
scgpt.model.model
scgpt.preprocess
scgpt.scbank
scgpt.scbank.data
scgpt.scbank.databank
scgpt.scbank.monitor
scgpt.scbank.setting
scgpt.tasks
scgpt.tasks.cell_emb
scgpt.tasks.grn
scgpt.tokenizer
scgpt.tokenizer.gene_tokenizer
scgpt.trainer
scgpt.utils
scgpt.utils.util
MVCDecoder (class in scgpt.model.model)
N
name (scgpt.scbank.data.DataTable attribute)
O
on_disk_format (scgpt.scbank.data.MetaInfo attribute)
on_disk_path (scgpt.scbank.data.MetaInfo attribute)
P
pad_batch() (in module scgpt.tokenizer.gene_tokenizer)
pad_token (scgpt.tokenizer.gene_tokenizer.GeneVocab property)
pad_token_id (scgpt.data_collator.DataCollator attribute)
pad_value (scgpt.data_collator.DataCollator attribute)
plot_metagene() (scgpt.tasks.grn.GeneEmbedding method)
plot_metagenes_scores() (scgpt.tasks.grn.GeneEmbedding method)
plot_similarities() (scgpt.tasks.grn.GeneEmbedding method)
PositionalEncoding (class in scgpt.model.generation_model)
(class in scgpt.model.model)
pred_perturb() (scgpt.model.generation_model.TransformerGenerator method)
predict() (in module scgpt.trainer)
prepare_data() (in module scgpt.trainer)
prepare_dataloader() (in module scgpt.trainer)
Preprocessor (class in scgpt.preprocess)
R
random_mask_value() (in module scgpt.tokenizer.gene_tokenizer)
read_embedding() (scgpt.tasks.grn.GeneEmbedding method)
read_vector() (scgpt.tasks.grn.GeneEmbedding static method)
remove_zero_rows (scgpt.scbank.setting.Setting attribute)
S
sampling (scgpt.data_collator.DataCollator attribute)
save() (scgpt.scbank.data.DataTable method)
(scgpt.scbank.data.MetaInfo method)
(scgpt.scbank.databank.DataBank method)
save_json() (scgpt.tokenizer.gene_tokenizer.GeneVocab method)
scgpt.data_collator
module
scgpt.data_sampler
module
scgpt.loss
module
scgpt.model
module
scgpt.model.dsbn
module
scgpt.model.generation_model
module
scgpt.model.grad_reverse
module
scgpt.model.model
module
scgpt.preprocess
module
scgpt.scbank
module
scgpt.scbank.data
module
scgpt.scbank.databank
module
scgpt.scbank.monitor
module
scgpt.scbank.setting
module
scgpt.tasks
module
scgpt.tasks.cell_emb
module
scgpt.tasks.grn
module
scgpt.tokenizer
module
scgpt.tokenizer.gene_tokenizer
module
scgpt.trainer
module
scgpt.utils
module
scgpt.utils.util
module
score_metagenes() (scgpt.tasks.grn.GeneEmbedding method)
SeqDataset (class in scgpt.trainer)
set_default_token() (scgpt.tokenizer.gene_tokenizer.GeneVocab method)
set_seed() (in module scgpt.utils.util)
Setting (class in scgpt.scbank.setting)
settings (scgpt.scbank.databank.DataBank attribute)
Similarity (class in scgpt.model.generation_model)
(class in scgpt.model.model)
study_ids (scgpt.scbank.data.MetaInfo attribute)
SubsetsBatchSampler (class in scgpt.data_sampler)
SubsetSequentialSampler (class in scgpt.data_sampler)
sync() (scgpt.scbank.databank.DataBank method)
T
tensorlist2tensor() (in module scgpt.utils.util)
test() (in module scgpt.trainer)
tokenize_and_pad_batch() (in module scgpt.tokenizer.gene_tokenizer)
tokenize_batch() (in module scgpt.tokenizer.gene_tokenizer)
track() (scgpt.scbank.databank.DataBank method)
train() (in module scgpt.trainer)
training (scgpt.model.dsbn.DomainSpecificBatchNorm1d attribute)
(scgpt.model.dsbn.DomainSpecificBatchNorm2d attribute)
(scgpt.model.generation_model.ClsDecoder attribute)
(scgpt.model.generation_model.GeneEncoder attribute)
(scgpt.model.generation_model.PositionalEncoding attribute)
(scgpt.model.generation_model.Similarity attribute)
(scgpt.model.generation_model.TransformerGenerator attribute)
(scgpt.model.model.AdversarialDiscriminator attribute)
(scgpt.model.model.BatchLabelEncoder attribute)
(scgpt.model.model.CategoryValueEncoder attribute)
(scgpt.model.model.ClsDecoder attribute)
(scgpt.model.model.ContinuousValueEncoder attribute)
(scgpt.model.model.ExprDecoder attribute)
(scgpt.model.model.FastTransformerEncoderWrapper attribute)
(scgpt.model.model.FlashTransformerEncoderLayer attribute)
(scgpt.model.model.GeneEncoder attribute)
(scgpt.model.model.MVCDecoder attribute)
(scgpt.model.model.PositionalEncoding attribute)
(scgpt.model.model.Similarity attribute)
(scgpt.model.model.TransformerModel attribute)
(scgpt.tokenizer.gene_tokenizer.GeneVocab attribute)
TransformerGenerator (class in scgpt.model.generation_model)
TransformerModel (class in scgpt.model.model)
U
update_datatables() (scgpt.scbank.databank.DataBank method)
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