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UNCURL 0.2.3 documentation
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Z
A
Argmax (class in uncurl.experiment_runner)
B
BasicNMF (class in uncurl.experiment_runner)
Bicluster (class in uncurl.experiment_runner)
binarize() (in module uncurl.qual2quant)
C
cell_normalize() (in module uncurl.preprocessing)
Cluster (class in uncurl.experiment_runner)
Cocluster (class in uncurl.experiment_runner)
cost_grad() (in module uncurl.scalable.state_estimation)
D
DBScan (class in uncurl.experiment_runner)
diffusion_mds() (in module uncurl.dimensionality_reduction)
dim_reduce() (in module uncurl.dimensionality_reduction)
dim_reduce_data() (in module uncurl.dimensionality_reduction)
E
EnsembleClusterPoissonSE (class in uncurl.experiment_runner)
EnsembleNMF (class in uncurl.experiment_runner)
EnsembleTsneLightLDASE (class in uncurl.experiment_runner)
EnsembleTsneNMF (class in uncurl.experiment_runner)
EnsembleTsnePoissonSE (class in uncurl.experiment_runner)
EnsembleTSVDPoissonSE (class in uncurl.experiment_runner)
F
fourier_series() (in module uncurl.lineage)
G
generate_nb_data() (in module uncurl.simulation)
generate_nb_state_data() (in module uncurl.simulation)
generate_nb_states() (in module uncurl.simulation)
generate_poisson_data() (in module uncurl.simulation)
generate_poisson_lineage() (in module uncurl.simulation)
generate_poisson_states() (in module uncurl.simulation)
generate_state_data() (in module uncurl.simulation)
generate_visualizations() (in module uncurl.experiment_runner)
generate_zip_data() (in module uncurl.simulation)
generate_zip_state_data() (in module uncurl.simulation)
graph_distances() (in module uncurl.lineage)
I
initialize_from_assignments() (in module uncurl.state_estimation)
initialize_means() (in module uncurl.state_estimation)
initialize_means_weights() (in module uncurl.state_estimation)
initialize_weights_nn() (in module uncurl.state_estimation)
K
KFoldNMF (class in uncurl.experiment_runner)
KM (class in uncurl.experiment_runner)
kmeans_pp() (in module uncurl.clustering)
L
LightLDASE (class in uncurl.experiment_runner)
lineage() (in module uncurl)
(in module uncurl.lineage)
LoadPreproc (class in uncurl.experiment_runner)
Log (class in uncurl.experiment_runner)
log1p() (in module uncurl.preprocessing)
log_norm_nmf() (in module uncurl.nmf_wrapper)
LogNMF (class in uncurl.experiment_runner)
LogNorm (class in uncurl.experiment_runner)
M
m_grad() (in module uncurl.scalable.state_estimation)
Magic (class in uncurl.experiment_runner)
max_variance_genes() (in module uncurl)
(in module uncurl.preprocessing)
mdl() (in module uncurl.evaluation)
mds() (in module uncurl)
(in module uncurl.dimensionality_reduction)
N
nb_cluster() (in module uncurl)
nb_estimate_state() (in module uncurl)
(in module uncurl.nb_state_estimation)
nmf_init() (in module uncurl.nmf_wrapper)
nne() (in module uncurl.evaluation)
norm_nmf() (in module uncurl.nmf_wrapper)
P
Pca (class in uncurl.experiment_runner)
PcaKm (class in uncurl.experiment_runner)
PLDASE (class in uncurl.experiment_runner)
poisson_cluster() (in module uncurl)
(in module uncurl.clustering)
poisson_dist() (in module uncurl.pois_ll)
poisson_estimate_state() (in module uncurl)
(in module uncurl.scalable.state_estimation)
(in module uncurl.state_estimation)
poisson_ll() (in module uncurl.pois_ll)
poisson_ll_2() (in module uncurl.pois_ll)
poisson_test() (in module uncurl.qual2quant)
PoissonCluster (class in uncurl.experiment_runner)
PoissonSE (class in uncurl.experiment_runner)
poly_curve() (in module uncurl.lineage)
Preprocess (class in uncurl.experiment_runner)
pseudotime() (in module uncurl)
(in module uncurl.lineage)
purity() (in module uncurl.evaluation)
Q
qualNorm() (in module uncurl)
(in module uncurl.qual2quant)
qualNorm_filter_genes() (in module uncurl.qual2quant)
qualNormGaussian() (in module uncurl.qual2quant)
R
run() (uncurl.experiment_runner.Argmax method)
(uncurl.experiment_runner.BasicNMF method)
(uncurl.experiment_runner.Bicluster method)
(uncurl.experiment_runner.Cluster method)
(uncurl.experiment_runner.Cocluster method)
(uncurl.experiment_runner.DBScan method)
(uncurl.experiment_runner.EnsembleClusterPoissonSE method)
(uncurl.experiment_runner.EnsembleNMF method)
(uncurl.experiment_runner.EnsembleTSVDPoissonSE method)
(uncurl.experiment_runner.EnsembleTsneLightLDASE method)
(uncurl.experiment_runner.EnsembleTsneNMF method)
(uncurl.experiment_runner.EnsembleTsnePoissonSE method)
(uncurl.experiment_runner.KFoldNMF method)
(uncurl.experiment_runner.KM method)
(uncurl.experiment_runner.LightLDASE method)
(uncurl.experiment_runner.LoadPreproc method)
(uncurl.experiment_runner.Log method)
(uncurl.experiment_runner.LogNMF method)
(uncurl.experiment_runner.LogNorm method)
(uncurl.experiment_runner.Magic method)
(uncurl.experiment_runner.PLDASE method)
(uncurl.experiment_runner.Pca method)
(uncurl.experiment_runner.PcaKm method)
(uncurl.experiment_runner.PoissonCluster method)
(uncurl.experiment_runner.PoissonSE method)
(uncurl.experiment_runner.Preprocess method)
(uncurl.experiment_runner.Simlr method)
(uncurl.experiment_runner.SimlrKm method)
(uncurl.experiment_runner.SimlrSmall method)
(uncurl.experiment_runner.TSVD method)
(uncurl.experiment_runner.Tsne method)
(uncurl.experiment_runner.TsneKm method)
(uncurl.experiment_runner.Zifa method)
run_experiment() (in module uncurl.experiment_runner)
run_state_estimation() (in module uncurl.run_se)
S
Simlr (class in uncurl.experiment_runner)
SimlrKm (class in uncurl.experiment_runner)
SimlrSmall (class in uncurl.experiment_runner)
sparse_mean_var() (in module uncurl.preprocessing)
sparse_poisson_ll() (in module uncurl.pois_ll)
T
Tsne (class in uncurl.experiment_runner)
TsneKm (class in uncurl.experiment_runner)
TSVD (class in uncurl.experiment_runner)
U
uncurl (module)
uncurl.clustering (module)
uncurl.dimensionality_reduction (module)
uncurl.evaluation (module)
uncurl.experiment_runner (module)
uncurl.lineage (module)
uncurl.nb_state_estimation (module)
uncurl.nmf_wrapper (module)
uncurl.pois_ll (module)
uncurl.preprocessing (module)
uncurl.qual2quant (module)
uncurl.run_se (module)
uncurl.scalable (module)
uncurl.scalable.state_estimation (module)
uncurl.simulation (module)
uncurl.state_estimation (module)
W
w_grad() (in module uncurl.scalable.state_estimation)
Z
Zifa (class in uncurl.experiment_runner)
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UNCURL 0.2.3 documentation
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