CoSpar
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Main
About CoSpar
API
Release notes
Tutorial
Installation
Getting Started
Loading data
Preprocessing
Clonal analysis
Transition map inference
Transition map analysis
Examples
Hematopoiesis
Reprogramming
Lung differentiation
Synthetic bifurcation
Simulate differentiation process
In vivo hematopoiesis (DARLIN data)
CoSpar
Index
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Index
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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P
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Q
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R
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S
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U
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V
B
barcode_heatmap() (in module cospar.pl)
bifurcation_model() (in module cospar.simulate)
C
check_adata_structure() (in module cospar.hf)
check_available_choices() (in module cospar.hf)
clonal_fate_bias() (in module cospar.pl)
(in module cospar.tl)
clonal_fates_across_time() (in module cospar.pl)
clonal_reports() (in module cospar.pl)
clones_on_manifold() (in module cospar.pl)
cospar
module
D
differential_genes() (in module cospar.tl)
E
embedding() (in module cospar.pl)
embedding_genes() (in module cospar.pl)
F
fate_bias() (in module cospar.pl)
(in module cospar.tl)
fate_biased_clones() (in module cospar.tl)
fate_coupling() (in module cospar.pl)
(in module cospar.tl)
fate_hierarchy() (in module cospar.pl)
(in module cospar.tl)
fate_map() (in module cospar.pl)
(in module cospar.tl)
fate_potency() (in module cospar.pl)
(in module cospar.tl)
G
gene_expression_dynamics() (in module cospar.pl)
gene_expression_heatmap() (in module cospar.pl)
gene_expression_on_manifold() (in module cospar.pl)
get_highly_variable_genes() (in module cospar.pp)
get_normalized_covariance() (in module cospar.tl)
get_state_info() (in module cospar.pp)
get_X_clone() (in module cospar.pp)
get_X_clone_with_reference_ordering() (in module cospar.hf)
get_X_emb() (in module cospar.pp)
get_X_pca() (in module cospar.pp)
H
hematopoiesis() (in module cospar.datasets)
hematopoiesis_130K() (in module cospar.datasets)
hematopoiesis_Gata1_states() (in module cospar.datasets)
hematopoiesis_subsampled() (in module cospar.datasets)
I
infer_Tmap_from_clonal_info_alone() (in module cospar.tmap)
infer_Tmap_from_multitime_clones() (in module cospar.tmap)
infer_Tmap_from_one_time_clones() (in module cospar.tmap)
infer_Tmap_from_state_info_alone() (in module cospar.tmap)
initialize_adata_object() (in module cospar.pp)
iterative_differentiation() (in module cospar.pl)
(in module cospar.tl)
L
linear_differentiation_model() (in module cospar.simulate)
lung() (in module cospar.datasets)
M
module
cospar
P
progenitor() (in module cospar.pl)
(in module cospar.tl)
Q
quantify_correlation_with_ground_truth_fate_bias_BifurcationModel() (in module cospar.simulate)
quantify_transition_peak_TPR_LinearDifferentiation() (in module cospar.simulate)
R
read() (in module cospar.hf)
refine_state_info_by_leiden_clustering() (in module cospar.pp)
refine_state_info_by_marker_genes() (in module cospar.pp)
remove_cell_cycle_correlated_genes() (in module cospar.pp)
reprogramming() (in module cospar.datasets)
reprogramming_Day0_3_28() (in module cospar.datasets)
S
save_map() (in module cospar.hf)
save_preprocessed_adata() (in module cospar.hf)
set_figure_params() (in module cospar.settings)
single_cell_transition() (in module cospar.pl)
synthetic_bifurcation() (in module cospar.datasets)
U
update_data_description() (in module cospar.hf)
update_time_ordering() (in module cospar.hf)
V
visualize_tree() (in module cospar.pl)
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