Getting Started
User Guide
API
FAQ
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Index
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A
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B
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C
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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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J
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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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W
_
__getitem__() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
A
AccessibilityTopicModel (class in mira.topics)
B
BayesianTuner (class in mira.topics)
C
compare_driver_TFs_plot() (in module mira.pl)
E
ExpressionTopicModel (class in mira.topics)
F
fetch_best_weights() (mira.topics.BayesianTuner method)
fetch_binding_sites() (in module mira.utils)
fetch_enrichments() (mira.topics.ExpressionTopicModel method)
fetch_factor_hits() (in module mira.utils)
fetch_factor_meta() (in module mira.utils)
fetch_gene_TSS_distances() (in module mira.utils)
fetch_ontologies() (in module mira.tl)
,
[1]
,
[2]
fetch_ontology() (in module mira.tl)
,
[1]
,
[2]
fetch_topic_enrichments() (mira.topics.ExpressionTopicModel method)
fetch_TSS_data() (in module mira.utils)
fetch_weights() (mira.topics.BayesianTuner method)
find_terminal_cells() (in module mira.time)
fit() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
(mira.topics.AccessibilityTopicModel method)
(mira.topics.BayesianTuner method)
(mira.topics.ExpressionTopicModel method)
FrankenCell_RNA() (in module mira.datasets)
G
GeneModel (class in mira.rp_model.rp_model)
get_branch_probabilities() (in module mira.time)
get_cell_pointwise_mutual_information() (in module mira.tl)
,
[1]
get_ChIP_hits_in_peaks() (in module mira.tl)
,
[1]
get_chromatin_differential() (in module mira.tl)
,
[1]
get_connected_components() (in module mira.time)
get_distance_to_TSS() (in module mira.tl)
,
[1]
get_enriched_TFs() (mira.topics.AccessibilityTopicModel method)
get_enrichments() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
get_hierarchical_umap_features() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
get_influential_local_peaks() (mira.rp_model.rp_model.GeneModel method)
get_learning_rate_bounds() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
get_model() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
get_motif_hits_in_peaks() (in module mira.tl)
,
[1]
get_motif_scores() (mira.topics.AccessibilityTopicModel method)
get_NITE_score_cells() (in module mira.tl)
,
[1]
get_NITE_score_genes() (in module mira.tl)
,
[1]
get_relative_norms() (in module mira.tl)
,
[1]
get_top_genes() (mira.topics.ExpressionTopicModel method)
get_topic_cross_correlation() (in module mira.tl)
,
[1]
get_transport_map() (in module mira.time)
get_tree_structure() (in module mira.time)
get_umap_features() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
gradient_tune() (in module mira.topics)
H
hg38_chrom_sizes() (in module mira.datasets)
hg38_tss_data() (in module mira.datasets)
I
impute() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
instantiate_model() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
J
join() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
L
LITE_Model (class in mira.rp)
,
[1]
load() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
(mira.topics.AccessibilityTopicModel class method)
(mira.topics.BayesianTuner class method)
(mira.topics.ExpressionTopicModel class method)
load_dir() (mira.rp.LITE_Model class method)
(mira.rp.NITE_Model class method)
M
make_joint_representation() (in module mira.utils)
,
[1]
,
[2]
make_model() (in module mira.topics)
mira
module
mira.tl.chip_scan
module
mira.tl.motif_scan
module
mm10_chrom_sizes() (in module mira.datasets)
mm10_tss_data() (in module mira.datasets)
module
mira
mira.tl.chip_scan
mira.tl.motif_scan
MouseBrainDataset() (in module mira.datasets)
N
NITE_Model (class in mira.rp)
,
[1]
normalize_diffmap() (in module mira.time)
P
parameters_ (mira.rp.LITE_Model property)
(mira.rp.NITE_Model property)
(mira.rp_model.rp_model.GeneModel property)
plot_chromatin_differential() (in module mira.pl)
plot_compare_topic_enrichments() (mira.topics.AccessibilityTopicModel method)
plot_disentanglement() (in module mira.pl)
plot_eigengap() (in module mira.pl)
plot_enrichments() (in module mira.pl)
(mira.topics.ExpressionTopicModel method)
plot_intermediate_values() (mira.topics.BayesianTuner method)
plot_learning_rate_bounds() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
plot_pareto_front() (mira.topics.BayesianTuner method)
plot_scatter_chromatin_differential() (in module mira.pl)
plot_stream() (in module mira.pl)
plot_topic_contributions() (in module mira.pl)
post_genelist() (in module mira.tl)
,
[1]
,
[2]
post_topic() (mira.topics.ExpressionTopicModel method)
post_topics() (mira.topics.ExpressionTopicModel method)
predict() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
(mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
pretty_sderr() (in module mira.utils)
probabilistic_isd() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
PseudotimeTrajectoryInferenceTutorial() (in module mira.datasets)
purge() (mira.topics.BayesianTuner method)
R
rank_genes() (mira.topics.ExpressionTopicModel method)
rank_modules() (mira.topics.ExpressionTopicModel method)
Redis (class in mira.topics)
S
save() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
(mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
score() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
set_device() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
set_learning_rates() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
ShareseqAnnotatedData() (in module mira.datasets)
ShareseqBaseData() (in module mira.datasets)
ShareseqRPModels() (in module mira.datasets)
ShareseqSkin_Ma2020() (in module mira.datasets)
ShareseqTopicModels() (in module mira.datasets)
show_gif() (in module mira.utils)
spawn_NITE_model() (mira.rp.LITE_Model method)
,
[1]
StreamGraphTutorial() (in module mira.datasets)
subset() (mira.rp.LITE_Model method)
(mira.rp.NITE_Model method)
subset_factors() (in module mira.utils)
summarize_mutual_information() (in module mira.tl)
,
[1]
T
to_cpu() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
to_gpu() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
trace_differentiation() (in module mira.time)
trim_learning_rate_bounds() (mira.topics.AccessibilityTopicModel method)
(mira.topics.ExpressionTopicModel method)
W
wide_view() (in module mira.utils)
write_bedgraph() (mira.rp_model.rp_model.GeneModel method)