CytofDR
v0.2.0
Getting Started
Installation Guide
Quickstart Guide
Tutorial
IO and Preprocessing with PyCytoData
DR Methods and Usage
Choosing a DR Method
Evaluation Metrics
Custom DR Evaluations
Save DR and Evaluation Results
Optimizations: PCD and ANNOY
Development
Contribution Guideline
Building and Testing
Development and Roadmap
Changelog
Releases
Recent Changes
License
Full API Reference
Full API Reference
Module: CytofDR.dr
Module: CytofDR.evaluation
Resources
References
Our Paper
Dr. Xinlei (Shery) Wang
Dr. Tao Wang
DBAI
GitHub
CytofDR
Index
Edit on GitHub
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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I
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K
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L
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M
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N
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O
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P
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R
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S
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U
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Z
A
add_custom_evaluation_result() (CytofDR.dr.Reductions method)
add_evaluation_metadata() (CytofDR.dr.Reductions method)
add_reduction() (CytofDR.dr.Reductions method)
Annoy (class in CytofDR.evaluation)
ARI() (CytofDR.evaluation.EvaluationMetrics static method)
B
build_annoy() (CytofDR.evaluation.Annoy static method)
(CytofDR.evaluation.EvaluationMetrics static method)
C
calinski_harabasz() (CytofDR.evaluation.EvaluationMetrics static method)
cluster() (CytofDR.dr.Reductions method)
correlation() (CytofDR.evaluation.EvaluationMetrics static method)
CytofDR.dr
module
CytofDR.evaluation
module
D
davies_bouldin() (CytofDR.evaluation.EvaluationMetrics static method)
E
embedding_concordance() (CytofDR.evaluation.EvaluationMetrics static method)
EMD() (CytofDR.evaluation.EvaluationMetrics static method)
evaluate() (CytofDR.dr.Reductions method)
EvaluationMetrics (class in CytofDR.evaluation)
F
FA() (CytofDR.dr.LinearMethods static method)
fit() (CytofDR.evaluation.PointClusterDistance method)
flatten() (CytofDR.evaluation.PointClusterDistance static method)
G
get_reduction() (CytofDR.dr.Reductions method)
grandprix() (CytofDR.dr.NonLinearMethods static method)
I
ICA() (CytofDR.dr.LinearMethods static method)
isomap() (CytofDR.dr.NonLinearMethods static method)
K
kernelPCA() (CytofDR.dr.NonLinearMethods static method)
KNN() (CytofDR.evaluation.EvaluationMetrics static method)
L
LinearMethods (class in CytofDR.dr)
LLE() (CytofDR.dr.NonLinearMethods static method)
load_annoy() (CytofDR.evaluation.Annoy static method)
M
MDS() (CytofDR.dr.NonLinearMethods static method)
module
CytofDR.dr
CytofDR.evaluation
N
neighborhood_agreement() (CytofDR.evaluation.EvaluationMetrics static method)
neighborhood_trustworthiness() (CytofDR.evaluation.EvaluationMetrics static method)
NMF() (CytofDR.dr.LinearMethods static method)
NMI() (CytofDR.evaluation.EvaluationMetrics static method)
NonLinearMethods (class in CytofDR.dr)
NPE() (CytofDR.evaluation.EvaluationMetrics static method)
O
open_tsne() (CytofDR.dr.NonLinearMethods static method)
P
PCA() (CytofDR.dr.LinearMethods static method)
phate() (CytofDR.dr.NonLinearMethods static method)
plot_reduction() (CytofDR.dr.Reductions method)
PointClusterDistance (class in CytofDR.evaluation)
R
random_forest() (CytofDR.evaluation.EvaluationMetrics static method)
rank_dr_methods() (CytofDR.dr.Reductions method)
rank_dr_methods_custom() (CytofDR.dr.Reductions method)
Reductions (class in CytofDR.dr)
reductions (CytofDR.dr.Reductions property)
residual_variance() (CytofDR.evaluation.EvaluationMetrics static method)
run_dr_methods() (in module CytofDR.dr)
S
SAUCIE() (CytofDR.dr.NonLinearMethods static method)
save_all_reductions() (CytofDR.dr.Reductions method)
save_annoy() (CytofDR.evaluation.Annoy static method)
save_evaluations() (CytofDR.dr.Reductions method)
save_reduction() (CytofDR.dr.Reductions method)
silhouette() (CytofDR.evaluation.EvaluationMetrics static method)
sklearn_tsne() (CytofDR.dr.NonLinearMethods static method)
spectral() (CytofDR.dr.NonLinearMethods static method)
U
UMAP() (CytofDR.dr.NonLinearMethods static method)
Z
ZIFA() (CytofDR.dr.LinearMethods static method)
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v: v0.2.0
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