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scRNA-seq analysis
scATAC-seq analysis
Multimodal analysis
Multimodal gene regulatory network
Batch correction (two batches)
Batch correction (multiple batches)
Multiomics integration
Generalized graph generation
Use edge weigthts
SIMBA on 1.3 million cells
SIMBA
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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H
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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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Q
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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
A
atac_10xpbmc5k() (in module simba.datasets)
atac_buenrostro2018() (in module simba.datasets)
atac_chen2019() (in module simba.datasets)
atac_cusanovich2018_subset() (in module simba.datasets)
B
binarize() (in module simba.pp)
C
cal_qc() (in module simba.pp)
cal_qc_atac() (in module simba.pp)
cal_qc_rna() (in module simba.pp)
compare_entities() (in module simba.tl)
D
discretize() (in module simba.pl)
(in module simba.tl)
E
embed() (in module simba.tl)
entity_barcode() (in module simba.pl)
entity_metrics() (in module simba.pl)
F
filter_cells_atac() (in module simba.pp)
filter_cells_rna() (in module simba.pp)
filter_features() (in module simba.pp)
filter_genes() (in module simba.pp)
filter_peaks() (in module simba.pp)
filter_samples() (in module simba.pp)
find_master_regulators() (in module simba.tl)
find_target_genes() (in module simba.tl)
G
gen_graph() (in module simba.tl)
gene_scores() (in module simba.tl)
H
hist() (in module simba.pl)
I
infer_edges() (in module simba.tl)
L
load_graph_stats() (in module simba)
load_pbg_config() (in module simba)
log_transform() (in module simba.pp)
M
module
simba
multiome_10xpbmc10k() (in module simba.datasets)
multiome_chen2019() (in module simba.datasets)
multiome_ma2020_fig4() (in module simba.datasets)
N
node_similarity() (in module simba.pl)
normalize() (in module simba.pp)
P
pbg_metrics() (in module simba.pl)
pbg_train() (in module simba.tl)
pca() (in module simba.pp)
pca_variance_ratio() (in module simba.pl)
pcs_features() (in module simba.pl)
Q
query() (in module simba.pl)
(in module simba.tl)
R
read_10x_h5() (in module simba)
read_csv() (in module simba)
read_embedding() (in module simba)
read_h5ad() (in module simba)
read_mtx() (in module simba)
rna_10xpmbc3k() (in module simba.datasets)
rna_baron2016() (in module simba.datasets)
rna_han2018() (in module simba.datasets)
rna_muraro2016() (in module simba.datasets)
rna_segerstolpe2016() (in module simba.datasets)
rna_tmc2018() (in module simba.datasets)
rna_wang2016() (in module simba.datasets)
rna_xin2016() (in module simba.datasets)
S
select_pcs() (in module simba.pp)
select_pcs_features() (in module simba.pp)
select_variable_genes() (in module simba.pp)
set_figure_params() (simba.settings method)
set_pbg_params() (simba.settings method)
set_workdir() (simba.settings method)
simba
module
softmax() (in module simba.tl)
svd_nodes() (in module simba.pl)
T
trim_edges() (in module simba.tl)
U
umap() (in module simba.pl)
(in module simba.tl)
V
variable_genes() (in module simba.pl)
violin() (in module simba.pl)
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