Index

A

add_continuous_mapping() (scmagnify.plotting.GRNVisualizer method), [1] add_custom_motif() (scmagnify.tools.MotifScanner method), [1], [2] add_genesets() (scmagnify.tools.FuncEnrich method), [1], [2]

add_module() (scmagnify.MSNGC method), [1], [2] add_motifs() (scmagnify.plotting.GenomeViewer method), [1] apply() (scmagnify.MSNGC method), [1], [2] axis (scmagnify.GRNMuData attribute)

B

barplot() (in module scmagnify.plotting), [1], [2] bfloat16() (scmagnify.MSNGC method), [1], [2]

buffers() (scmagnify.MSNGC method), [1], [2] build_metacells_SEACells() (in module scmagnify.tools), [1], [2]

C

call_super_init (scmagnify.MSNGC attribute), [1], [2] children() (scmagnify.MSNGC method), [1], [2] chromatin_constraint() (in module scmagnify), [1], [2] circosplot() (in module scmagnify.plotting), [1], [2] compile() (scmagnify.MSNGC method), [1] compute_activity() (scmagnify.tools.RegDecomp method), [1], [2]

connect_peaks_genes() (in module scmagnify.tools), [1], [2] convert_motif_format() (in module scmagnify.tools), [1], [2] copy() (scmagnify.GRNMuData method) cp_decomposition() (scmagnify.tools.RegDecomp method), [1], [2] cpu() (scmagnify.MSNGC method), [1], [2] cuda() (scmagnify.MSNGC method), [1], [2]

D

distplot() (in module scmagnify.plotting), [1], [2]

double() (scmagnify.MSNGC method), [1], [2] dump_patches (scmagnify.MSNGC attribute), [1], [2]

E

estimate_lags() (scmagnify.MAGNI method), [1], [2] eval() (scmagnify.MSNGC method), [1], [2] example_interactive_plot() (scmagnify.plotting.GRNVisualizer method), [1]

export() (scmagnify.plotting.GRNVisualizer method), [1] export_motifs() (scmagnify.tools.MotifScanner method), [1], [2] extra_repr() (scmagnify.MSNGC method), [1], [2] extract_regfactor_genes() (in module scmagnify.tools), [1], [2]

F

filename (scmagnify.GRNMuData attribute) filter() (scmagnify.GRNMuData method) filter_genesets() (scmagnify.tools.FuncEnrich method), [1], [2]

float() (scmagnify.MSNGC method), [1], [2] forward() (scmagnify.MSNGC method), [1], [2] FuncEnrich (class in scmagnify.tools), [1], [2]

G

GenomeViewer (class in scmagnify.plotting), [1] get_buffer() (scmagnify.MSNGC method), [1], [2] get_extra_state() (scmagnify.MSNGC method), [1], [2] get_network_score() (in module scmagnify.tools), [1], [2] get_overlap_genes() (scmagnify.tools.FuncEnrich method), [1], [2]

get_parameter() (scmagnify.MSNGC method), [1], [2] get_submodule() (scmagnify.MSNGC method), [1], [2] get_tensor (scmagnify.tools.RegDecomp attribute), [1], [2] GRNMuData (class in scmagnify) GRNVisualizer (class in scmagnify.plotting), [1]

H

half() (scmagnify.MSNGC method), [1], [2]

heatmap() (in module scmagnify.plotting), [1], [2]

I

import_basalGRN() (in module scmagnify), [1], [2] import_motifs() (scmagnify.tools.MotifScanner method), [1], [2] infer_signal_pairs() (in module scmagnify.tools), [1], [2]

init_weights() (scmagnify.MSNGC method), [1], [2] ipu() (scmagnify.MSNGC method), [1], [2] isbacked (scmagnify.GRNMuData attribute)

L

lineage_classifer() (in module scmagnify.tools), [1], [2] load() (scmagnify.MAGNI method), [1], [2]

load_network() (scmagnify.plotting.GRNVisualizer method), [1] load_state_dict() (scmagnify.MSNGC method), [1], [2]

M

MAGNI (class in scmagnify), [1], [2] match() (scmagnify.tools.MotifScanner method), [1], [2] module scmagnify.datasets scmagnify.logging scmagnify.models, [1] scmagnify.plotting, [1] scmagnify.settings, [1] scmagnify.tools, [1] scmagnify.utils

modules() (scmagnify.MSNGC method), [1], [2] MotifScanner (class in scmagnify.tools), [1], [2] MSNGC (class in scmagnify), [1], [2] mtia() (scmagnify.MSNGC method), [1]

N

n_mod (scmagnify.GRNMuData attribute) n_obs (scmagnify.GRNMuData attribute) n_var (scmagnify.GRNMuData attribute) n_vars (scmagnify.GRNMuData attribute)

named_buffers() (scmagnify.MSNGC method), [1], [2] named_children() (scmagnify.MSNGC method), [1], [2] named_modules() (scmagnify.MSNGC method), [1], [2] named_parameters() (scmagnify.MSNGC method), [1], [2] normalization() (scmagnify.tools.RegDecomp method), [1], [2]

O

obs (scmagnify.GRNMuData attribute) obs_keys() (scmagnify.GRNMuData method) obs_names (scmagnify.GRNMuData attribute) obs_names_make_unique() (scmagnify.GRNMuData method)

obs_vector() (scmagnify.GRNMuData method) obsm (scmagnify.GRNMuData attribute) obsm_keys() (scmagnify.GRNMuData method) obsmap (scmagnify.GRNMuData attribute) obsp (scmagnify.GRNMuData attribute)

P

parameters() (scmagnify.MSNGC method), [1], [2] partial_ordering() (in module scmagnify), [1], [2]

plot() (scmagnify.plotting.GenomeViewer method), [1] (scmagnify.plotting.GRNVisualizer method), [1] prepare_network() (scmagnify.plotting.GRNVisualizer method), [1]

R

rankplot() (in module scmagnify.plotting), [1], [2] RegDecomp (class in scmagnify.tools), [1], [2] register_backward_hook() (scmagnify.MSNGC method), [1], [2] register_buffer() (scmagnify.MSNGC method), [1], [2] register_forward_hook() (scmagnify.MSNGC method), [1], [2] register_forward_pre_hook() (scmagnify.MSNGC method), [1], [2] register_full_backward_hook() (scmagnify.MSNGC method), [1], [2] register_full_backward_pre_hook() (scmagnify.MSNGC method), [1], [2] register_load_state_dict_post_hook() (scmagnify.MSNGC method), [1], [2]

register_load_state_dict_pre_hook() (scmagnify.MSNGC method), [1] register_module() (scmagnify.MSNGC method), [1], [2] register_parameter() (scmagnify.MSNGC method), [1], [2] register_state_dict_post_hook() (scmagnify.MSNGC method), [1] register_state_dict_pre_hook() (scmagnify.MSNGC method), [1], [2] regulation_inference() (scmagnify.MAGNI method), [1], [2] rename_regfactors() (scmagnify.tools.RegDecomp method), [1], [2] requires_grad_() (scmagnify.MSNGC method), [1], [2] run_ora() (scmagnify.tools.FuncEnrich method), [1], [2]

S

save() (scmagnify.MAGNI method), [1], [2] scmagnify.datasets module scmagnify.logging module scmagnify.models module, [1] scmagnify.plotting module, [1] scmagnify.settings module, [1] scmagnify.tools module, [1]

scmagnify.utils module select_paga_path() (in module scmagnify.tools), [1], [2] set_extra_state() (scmagnify.MSNGC method), [1], [2] set_submodule() (scmagnify.MSNGC method), [1] shape (scmagnify.GRNMuData attribute) share_memory() (scmagnify.MSNGC method), [1], [2] show_motif_databases() (scmagnify.tools.MotifScanner method), [1], [2] state_dict() (scmagnify.MSNGC method), [1], [2] strings_to_categoricals() (scmagnify.GRNMuData method) stripplot() (in module scmagnify.plotting), [1], [2]

T

T_destination (scmagnify.MSNGC attribute), [1], [2] test_association() (in module scmagnify.tools), [1], [2] to() (scmagnify.MSNGC method), [1], [2] to_cyto() (scmagnify.GRNMuData method) to_empty() (scmagnify.MSNGC method), [1], [2] to_matrix() (scmagnify.GRNMuData method)

to_nx() (scmagnify.GRNMuData method) train() (scmagnify.MAGNI method), [1], [2] (scmagnify.MSNGC method), [1], [2] training (scmagnify.MSNGC attribute), [1], [2] trendplot() (in module scmagnify.plotting), [1], [2] tucker_decomposition() (scmagnify.tools.RegDecomp method), [1], [2] type() (scmagnify.MSNGC method), [1], [2]

U

uns_keys() (scmagnify.GRNMuData method) update() (scmagnify.GRNMuData method)

update_obs() (scmagnify.GRNMuData method) update_var() (scmagnify.GRNMuData method)

V

var (scmagnify.GRNMuData attribute) var_keys() (scmagnify.GRNMuData method) var_names (scmagnify.GRNMuData attribute) var_names_make_unique() (scmagnify.GRNMuData method)

var_vector() (scmagnify.GRNMuData method) varm (scmagnify.GRNMuData attribute) varm_keys() (scmagnify.GRNMuData method) varmap (scmagnify.GRNMuData attribute) varp (scmagnify.GRNMuData attribute)

W

write() (scmagnify.GRNMuData method)

write_h5mu() (scmagnify.GRNMuData method) write_zarr() (scmagnify.GRNMuData method)

X

xpu() (scmagnify.MSNGC method), [1], [2]

Z

zero_grad() (scmagnify.MSNGC method), [1], [2]