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Overview
About SIMBA
Installation
API
Release notes
Citation
SIMBA primer
Basic concepts
Output
Tutorials
scRNA-seq analysis
scATAC-seq analysis
Multimodal analysis
Multimodal gene regulatory network
Batch correction (two batches)
Batch correction (multiple batches)
Multiomics integration
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
|
I
|
L
|
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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