scglue
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Contents:
Installation guide
Tutorials
Example datasets
API documentation
Release notes
Developer guide
Credits
scglue
Index
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Index
A
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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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I
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L
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M
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N
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P
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R
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S
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T
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U
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V
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W
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Z
A
accept_shuffle() (scglue.models.data.AnnDataset method)
(scglue.models.data.ArrayDataset method)
(scglue.models.data.Dataset method)
(scglue.models.data.GraphDataset method)
adopt_pretrained_model() (scglue.models.scclue.SCCLUEModel method)
(scglue.models.scglue.SCGLUEModel method)
aggregate_obs() (in module scglue.data)
all_counts() (in module scglue.num)
AnnDataset (class in scglue.models.data)
ArrayDataset (class in scglue.models.data)
attach() (scglue.models.base.TrainingPlugin method)
(scglue.models.plugins.EarlyStopping method)
(scglue.models.plugins.LRScheduler method)
(scglue.models.plugins.Tensorboard method)
autodevice() (in module scglue.models.nn)
avg_silhouette_width() (in module scglue.metrics)
avg_silhouette_width_batch() (in module scglue.metrics)
B
BatchedTransferrable (class in scglue.models.scclue)
Bed (class in scglue.genomics)
bedmap2anndata() (in module scglue.data)
BernoulliDataDecoder (class in scglue.models.scclue)
C
check() (scglue.check.Checker method)
(scglue.check.CmdChecker method)
(scglue.check.ModuleChecker method)
check_deps() (in module scglue.check)
check_graph() (in module scglue.graph)
Checker (class in scglue.check)
cis_regulatory_ranking() (in module scglue.genomics)
Classifier (class in scglue.models.sc)
(class in scglue.models.scclue)
clean() (scglue.models.data.Dataset method)
CmdChecker (class in scglue.check)
col_pcc() (in module scglue.num)
col_spr() (in module scglue.num)
col_var() (in module scglue.num)
collapse_multigraph() (in module scglue.graph)
compile() (scglue.models.base.Model method)
(scglue.models.scclue.SCCLUEModel method)
(scglue.models.scglue.PairedSCGLUEModel method)
(scglue.models.scglue.SCGLUEModel method)
compose_multigraph() (in module scglue.graph)
CompositeDataEncoder (class in scglue.models.scclue)
compute_dist() (scglue.models.scclue.BernoulliDataDecoder method)
(scglue.models.scclue.DataDecoder method)
(scglue.models.scclue.MSEDataDecoder method)
(scglue.models.scclue.NBDataDecoder method)
(scglue.models.scclue.NormalDataDecoder method)
(scglue.models.scclue.RMSEDataDecoder method)
(scglue.models.scclue.ZILNDataDecoder method)
(scglue.models.scclue.ZINDataDecoder method)
compute_l() (scglue.models.sc.DataEncoder method)
(scglue.models.sc.NBDataEncoder method)
(scglue.models.sc.VanillaDataEncoder method)
(scglue.models.scclue.CompositeDataEncoder method)
(scglue.models.scclue.NBCompositeDataEncoder method)
(scglue.models.scclue.VanillaCompositeDataEncoder method)
compute_losses() (scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
(scglue.models.scglue.PairedSCGLUETrainer method)
(scglue.models.scglue.SCGLUETrainer method)
ConfigManager (class in scglue.utils)
configure_dataset() (in module scglue.models)
ConstrainedDataFrame (class in scglue.utils)
count_prep() (in module scglue.data)
cov_mat() (in module scglue.num)
cross_predict() (scglue.models.scclue.SCCLUEModel method)
D
DataDecoder (class in scglue.models.glue)
(class in scglue.models.sc)
(class in scglue.models.scclue)
DataEncoder (class in scglue.models.glue)
(class in scglue.models.sc)
DataLoader (class in scglue.models.data)
Dataset (class in scglue.models.data)
decode_data() (scglue.models.scglue.SCGLUEModel method)
DelayedKeyboardInterrupt (class in scglue.utils)
densify() (in module scglue.num)
Discriminator (class in scglue.models.glue)
(class in scglue.models.sc)
(class in scglue.models.scclue)
dist_power_decay() (in module scglue.genomics)
E
EarlyStopping (class in scglue.models.plugins)
ElementDataEncoder (class in scglue.models.scclue)
encode_data() (scglue.models.scclue.SCCLUEModel method)
(scglue.models.scglue.SCGLUEModel method)
encode_graph() (scglue.models.scglue.SCGLUEModel method)
ens_trim_version() (in module scglue.genomics)
estimate_balancing_weight() (in module scglue.data)
expand() (scglue.genomics.Bed method)
extract_rank_genes_groups() (in module scglue.data)
F
fit() (scglue.models.base.Model method)
(scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUEModel method)
(scglue.models.scclue.SCCLUETrainer method)
(scglue.models.scglue.SCGLUEModel method)
fit_SCGLUE() (in module scglue.models)
format_data() (scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
(scglue.models.scglue.PairedSCGLUETrainer method)
(scglue.models.scglue.SCGLUETrainer method)
forward() (scglue.models.glue.DataDecoder method)
(scglue.models.glue.DataEncoder method)
(scglue.models.glue.Discriminator method)
(scglue.models.glue.GLUE method)
(scglue.models.glue.GraphDecoder method)
(scglue.models.glue.GraphEncoder method)
(scglue.models.glue.Prior method)
(scglue.models.nn.GraphAttent method)
(scglue.models.nn.GraphConv method)
(scglue.models.sc.DataDecoder method)
(scglue.models.sc.DataEncoder method)
(scglue.models.sc.Discriminator method)
(scglue.models.sc.GraphDecoder method)
(scglue.models.sc.GraphEncoder method)
(scglue.models.sc.IndDataDecoder method)
(scglue.models.sc.NBDataDecoder method)
(scglue.models.sc.NormalDataDecoder method)
(scglue.models.sc.Prior method)
(scglue.models.sc.ZILNDataDecoder method)
(scglue.models.sc.ZINBDataDecoder method)
(scglue.models.sc.ZINDataDecoder method)
(scglue.models.scclue.CompositeDataEncoder method)
(scglue.models.scclue.DataDecoder method)
(scglue.models.scclue.Discriminator method)
(scglue.models.scclue.ElementDataEncoder method)
(scglue.models.scclue.SCCLUE method)
foscttm() (in module scglue.metrics)
freeze_cells() (scglue.models.scglue.SCGLUEModel method)
freeze_running_stats() (in module scglue.models.nn)
G
get_chained_attr() (in module scglue.utils)
get_chr_len_from_fai() (in module scglue.genomics)
get_default_numpy_dtype() (in module scglue.models.nn)
get_gene_annotation() (in module scglue.data)
get_logger() (scglue.utils.LogManager method)
get_losses() (scglue.models.base.Model method)
(scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scglue.SCGLUEModel method)
get_metacells() (in module scglue.data)
get_rs() (in module scglue.utils)
GLUE (class in scglue.models.glue)
GLUETrainer (class in scglue.models.glue)
graph2triplet() (scglue.models.data.GraphDataset method)
graph_connectivity() (in module scglue.metrics)
GraphAttent (class in scglue.models.nn)
GraphConv (class in scglue.models.nn)
GraphDataset (class in scglue.models.data)
GraphDecoder (class in scglue.models.glue)
(class in scglue.models.sc)
GraphEncoder (class in scglue.models.glue)
(class in scglue.models.sc)
Gtf (class in scglue.genomics)
I
IndDataDecoder (class in scglue.models.sc)
IndNBDataDecoder (class in scglue.models.sc)
IndNormalDataDocoder (class in scglue.models.sc)
IndSCGLUE (class in scglue.models.scglue)
IndZILNDataDecoder (class in scglue.models.sc)
IndZINBDataDecoder (class in scglue.models.sc)
IndZINDataDecoder (class in scglue.models.sc)
integration_consistency() (in module scglue.models.dx)
interval_dist() (in module scglue.genomics)
L
load_model() (in module scglue.models)
load_state_dict() (scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
log_prob() (scglue.models.prob.MSE method)
(scglue.models.prob.RMSE method)
(scglue.models.prob.ZILN method)
(scglue.models.prob.ZIN method)
(scglue.models.prob.ZINB method)
logged() (in module scglue.utils)
LogManager (class in scglue.utils)
LRScheduler (class in scglue.models.plugins)
lsi() (in module scglue.data)
M
mean_average_precision() (in module scglue.metrics)
metacell_corr() (in module scglue.data)
metacell_regr() (in module scglue.data)
Model (class in scglue.models.base)
module
scglue
scglue.check
scglue.data
scglue.genomics
scglue.graph
scglue.metrics
scglue.models
scglue.models.base
scglue.models.data
scglue.models.dx
scglue.models.glue
scglue.models.nn
scglue.models.plugins
scglue.models.prob
scglue.models.sc
scglue.models.scclue
scglue.models.scglue
scglue.num
scglue.plot
scglue.typehint
scglue.utils
ModuleChecker (class in scglue.check)
MSE (class in scglue.models.prob)
MSEDataDecoder (class in scglue.models.scclue)
N
NBCompositeDataEncoder (class in scglue.models.scclue)
NBDataDecoder (class in scglue.models.sc)
(class in scglue.models.scclue)
NBDataEncoder (class in scglue.models.sc)
neighbor_conservation() (in module scglue.metrics)
NormalDataDecoder (class in scglue.models.sc)
(class in scglue.models.scclue)
normalize() (scglue.models.sc.DataEncoder method)
(scglue.models.sc.NBDataEncoder method)
(scglue.models.sc.VanillaDataEncoder method)
(scglue.models.scclue.CompositeDataEncoder method)
(scglue.models.scclue.NBCompositeDataEncoder method)
(scglue.models.scclue.VanillaCompositeDataEncoder method)
normalize_edges() (in module scglue.num)
normalized_mutual_info() (in module scglue.metrics)
nucleotide_content() (scglue.genomics.Bed method)
P
PairedSCGLUEModel (class in scglue.models.scglue)
PairedSCGLUETrainer (class in scglue.models.scglue)
ParallelDataLoader (class in scglue.models.data)
pcc_mat() (in module scglue.num)
prc() (in module scglue.plot)
prepare_shuffle() (scglue.models.data.Dataset method)
Prior (class in scglue.models.glue)
(class in scglue.models.sc)
prob_or() (in module scglue.num)
prod() (in module scglue.num)
propose_shuffle() (scglue.models.data.AnnDataset method)
(scglue.models.data.ArrayDataset method)
(scglue.models.data.Dataset method)
(scglue.models.data.GraphDataset method)
R
random_split() (scglue.models.data.AnnDataset method)
(scglue.models.data.ArrayDataset method)
reachable_vertices() (in module scglue.graph)
read_bed() (in module scglue.genomics)
(scglue.genomics.Bed class method)
read_ctx_grn() (in module scglue.genomics)
read_gtf() (in module scglue.genomics)
(scglue.genomics.Gtf class method)
rectify() (scglue.genomics.Bed class method)
(scglue.genomics.Gtf class method)
(scglue.utils.ConstrainedDataFrame class method)
register_prob_model() (in module scglue.models.scclue)
(in module scglue.models.scglue)
regulatory_inference() (in module scglue.genomics)
report_metrics() (scglue.models.base.Trainer method)
RMSE (class in scglue.models.prob)
RMSEDataDecoder (class in scglue.models.scclue)
rna_anchored_guidance_graph() (in module scglue.genomics)
rna_anchored_prior_graph() (in module scglue.genomics)
roc() (in module scglue.plot)
run_command() (in module scglue.utils)
S
sankey() (in module scglue.plot)
save() (scglue.models.base.Model method)
SCCLUE (class in scglue.models.scclue)
SCCLUEModel (class in scglue.models.scclue)
SCCLUETrainer (class in scglue.models.scclue)
scglue
module
SCGLUE (class in scglue.models.scglue)
scglue.check
module
scglue.data
module
scglue.genomics
module
scglue.graph
module
scglue.metrics
module
scglue.models
module
scglue.models.base
module
scglue.models.data
module
scglue.models.dx
module
scglue.models.glue
module
scglue.models.nn
module
scglue.models.plugins
module
scglue.models.prob
module
scglue.models.sc
module
scglue.models.scclue
module
scglue.models.scglue
module
scglue.num
module
scglue.plot
module
scglue.typehint
module
scglue.utils
module
SCGLUEModel (class in scglue.models.scglue)
SCGLUETrainer (class in scglue.models.scglue)
set_publication_params() (in module scglue.plot)
seurat_alignment_score() (in module scglue.metrics)
shuffle() (scglue.models.data.Dataset method)
shuffle_worker() (scglue.models.data.Dataset method)
sigmoid() (in module scglue.num)
SingletonMeta (class in scglue.utils)
split_attribute() (scglue.genomics.Gtf method)
spr_mat() (in module scglue.num)
state_dict() (scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
strand_specific_end_site() (scglue.genomics.Bed method)
strand_specific_start_site() (scglue.genomics.Bed method)
T
Tensorboard (class in scglue.models.plugins)
tfidf() (in module scglue.num)
to_bed() (scglue.genomics.Gtf method)
to_bedtool() (scglue.genomics.Bed method)
train_step() (scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
(scglue.models.scglue.SCGLUETrainer method)
Trainer (class in scglue.models.base)
TrainingPlugin (class in scglue.models.base)
transfer_labels() (in module scglue.data)
transfer_weights_from() (scglue.models.scclue.BatchedTransferrable method)
(scglue.models.scclue.SCCLUE method)
(scglue.models.scclue.Transferrable method)
Transferrable (class in scglue.models.scclue)
U
unfreeze_cells() (scglue.models.scglue.SCGLUEModel method)
upgrade() (scglue.models.base.Model method)
(scglue.models.scglue.SCGLUEModel method)
V
val_step() (scglue.models.base.Trainer method)
(scglue.models.glue.GLUETrainer method)
(scglue.models.scclue.SCCLUETrainer method)
VanillaCompositeDataEncoder (class in scglue.models.scclue)
VanillaDataEncoder (class in scglue.models.sc)
verify() (scglue.genomics.Bed class method)
(scglue.genomics.Gtf class method)
(scglue.utils.ConstrainedDataFrame class method)
vertex_degrees() (in module scglue.num)
W
window_graph() (in module scglue.genomics)
write_bed() (scglue.genomics.Bed method)
write_links() (in module scglue.genomics)
write_scenic_feather() (in module scglue.genomics)
Z
ZILN (class in scglue.models.prob)
ZILNDataDecoder (class in scglue.models.sc)
(class in scglue.models.scclue)
ZIN (class in scglue.models.prob)
ZINB (class in scglue.models.prob)
ZINBDataDecoder (class in scglue.models.sc)
ZINDataDecoder (class in scglue.models.sc)
(class in scglue.models.scclue)
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