scedar
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Read data
Exploratory Data Analysis
Check dimensions and data
Create an instance of scedar data structure
t-SNE
UMAP
Clustering
Visualize pairwise distance matrix
Visualize t-SNE
Identify cluster separating genes
K-nearest neighbors
Impute gene dropouts
Detect rare samples
API Reference Manual
scedar
scedar.cluster
scedar.cluster.mirac
scedar.cluster.community
scedar.cluster.community_mirac
scedar.eda
scedar.eda.mdl
scedar.eda.mtype
scedar.eda.plot
scedar.eda.sdm
scedar.eda.sfm
scedar.eda.slcs
scedar.eda.stats
scedar.knn
scedar.knn.detection
scedar.knn.imputation
scedar.utils
Changelog
[0.2.0] - Feb 11, 2020
Changed
Added
[0.1.7] - Jul 2, 2019
Changed
[0.1.6] - Jan 2, 2019
Added
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scedar
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Index
_
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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
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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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P
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R
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S
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T
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U
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X
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Z
_
_aff_scale (scedar.cluster.community.Community attribute)
_bw_method (scedar.eda.mdl.GKdeMdl attribute)
_cm_clp_x (scedar.cluster.community_mirac.CommunityMIRAC attribute)
_cm_res (scedar.cluster.community_mirac.CommunityMIRAC attribute)
_d (scedar.cluster.community_mirac.CommunityMIRAC attribute)
(scedar.eda.sdm.SampleDistanceMatrix attribute)
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
_encode_type (scedar.cluster.mirac.MIRAC attribute)
_fids (scedar.cluster.community_mirac.CommunityMIRAC attribute)
(scedar.eda.sdm.SampleDistanceMatrix attribute)
(scedar.eda.sfm.SampleFeatureMatrix attribute)
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
_graph (scedar.cluster.community.Community attribute)
_hac_tree (scedar.cluster.mirac.MIRAC attribute)
_hnsw_index_lut (scedar.eda.sdm.SampleDistanceMatrix attribute)
_index_params (scedar.cluster.community.Community attribute)
_is_sparse (scedar.eda.sfm.SampleFeatureMatrix attribute)
_k (scedar.cluster.community.Community attribute)
_kde (scedar.eda.mdl.GKdeMdl attribute)
_knn_ng_lut (scedar.eda.sdm.SampleDistanceMatrix attribute)
_la_res (scedar.cluster.community.Community attribute)
_labs (scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
_last_k (scedar.eda.sdm.SampleDistanceMatrix attribute)
_last_knns (scedar.eda.sdm.SampleDistanceMatrix attribute)
_last_tsne (scedar.eda.sdm.SampleDistanceMatrix attribute)
_logdens (scedar.eda.mdl.GKdeMdl attribute)
_mdl_method (scedar.cluster.mirac.MIRAC attribute)
(scedar.eda.slcs.MDLSingleLabelClassifiedSamples attribute)
_metric (scedar.eda.sdm.SampleDistanceMatrix attribute)
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
_min_cl_n (scedar.cluster.mirac.MIRAC attribute)
_mirac_res (scedar.cluster.community_mirac.CommunityMIRAC attribute)
_n (scedar.eda.mdl.GKdeMdl attribute)
(scedar.eda.mdl.Mdl attribute)
_nprocs (scedar.cluster.community_mirac.CommunityMIRAC attribute)
_query_params (scedar.cluster.community.Community attribute)
_res_lut (scedar.knn.detection.RareSampleDetection attribute)
(scedar.knn.imputation.FeatureImputation attribute)
_run_log (scedar.cluster.mirac.MIRAC attribute)
_sdm (scedar.cluster.community.Community attribute)
(scedar.cluster.mirac.MIRAC attribute)
(scedar.knn.detection.RareSampleDetection attribute)
(scedar.knn.imputation.FeatureImputation attribute)
_sids (scedar.cluster.community_mirac.CommunityMIRAC attribute)
(scedar.eda.sdm.SampleDistanceMatrix attribute)
(scedar.eda.sfm.SampleFeatureMatrix attribute)
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
_tsne_lut (scedar.eda.sdm.SampleDistanceMatrix attribute)
_use_hnsw (scedar.cluster.community.Community attribute)
_use_pca (scedar.cluster.community.Community attribute)
_verbose (scedar.cluster.community_mirac.CommunityMIRAC attribute)
_x (scedar.cluster.community_mirac.CommunityMIRAC attribute)
(scedar.eda.mdl.GKdeMdl attribute)
(scedar.eda.mdl.Mdl attribute)
(scedar.eda.sdm.SampleDistanceMatrix attribute)
(scedar.eda.sfm.SampleFeatureMatrix attribute)
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
B
bandwidth (scedar.eda.mdl.GKdeMdl attribute)
(scedar.eda.mdl.ZeroIGKdeMdl attribute)
bi_partition() (scedar.eda.sdm.HClustTree method)
bidir_ReLU() (in module scedar.eda.stats)
C
check_is_valid_labs() (in module scedar.eda.mtype)
check_is_valid_sfids() (in module scedar.eda.mtype)
cluster_id_to_lab_list() (scedar.eda.sdm.HClustTree static method)
cluster_mdl (scedar.eda.slcs.MDLSingleLabelClassifiedSamples.LabMdlResult attribute)
cluster_scatter() (in module scedar.eda.plot)
collapse_clusters() (scedar.cluster.community_mirac.CommunityMIRAC static method)
Community (class in scedar.cluster.community)
CommunityMIRAC (class in scedar.cluster.community_mirac)
compute_cluster_mdl() (scedar.eda.slcs.MDLSingleLabelClassifiedSamples static method)
correlation_pdist() (scedar.eda.sdm.SampleDistanceMatrix static method)
cosine_pdist() (scedar.eda.sdm.SampleDistanceMatrix static method)
count() (scedar.eda.sdm.HClustTree method)
cross_labs() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
D
d (scedar.eda.sdm.SampleDistanceMatrix attribute)
detect_rare_samples() (scedar.knn.detection.RareSampleDetection method)
dict_str_key() (in module scedar.utils)
dmat_heatmap() (scedar.cluster.mirac.MIRAC method)
(scedar.eda.slcs.SingleLabelClassifiedSamples method)
E
encode() (scedar.eda.mdl.GKdeMdl method)
(scedar.eda.mdl.Mdl method)
(scedar.eda.mdl.MultinomialMdl method)
(scedar.eda.mdl.ZeroIGKdeMdl method)
(scedar.eda.mdl.ZeroIMdl method)
(scedar.eda.mdl.ZeroIMultinomialMdl method)
(scedar.eda.slcs.MDLSingleLabelClassifiedSamples method)
F
f_cv() (scedar.eda.sfm.SampleFeatureMatrix method)
f_cv_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
f_gc() (scedar.eda.sfm.SampleFeatureMatrix method)
f_gc_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
f_id_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
f_id_regression_scatter() (scedar.eda.sfm.SampleFeatureMatrix method)
f_id_to_ind() (scedar.eda.sfm.SampleFeatureMatrix method)
f_id_x_vec() (scedar.eda.sfm.SampleFeatureMatrix method)
f_ind_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
f_ind_regression_scatter() (scedar.eda.sfm.SampleFeatureMatrix method)
f_ind_x_pair() (scedar.eda.sfm.SampleFeatureMatrix method)
f_ind_x_vec() (scedar.eda.sfm.SampleFeatureMatrix method)
f_n_above_threshold() (scedar.eda.sfm.SampleFeatureMatrix method)
f_n_above_threshold_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
f_sum() (scedar.eda.sfm.SampleFeatureMatrix method)
f_sum_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
feature_importance_across_labs() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
feature_importance_distintuishing_labs() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
feature_importance_each_lab() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
feature_swarm_plot() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
FeatureImputation (class in scedar.knn.imputation)
fids (scedar.eda.sfm.SampleFeatureMatrix attribute)
filter_1d_inds() (scedar.eda.sfm.SampleFeatureMatrix static method)
filter_min_class_n() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
G
gaussian_kde_logdens() (scedar.eda.mdl.GKdeMdl static method)
gc1d() (in module scedar.eda.stats)
get_tsne_kv() (scedar.eda.sdm.SampleDistanceMatrix method)
GKdeMdl (class in scedar.eda.mdl)
H
hclust_linkage() (scedar.eda.sdm.HClustTree static method)
hclust_tree() (scedar.eda.sdm.HClustTree static method)
HClustTree (class in scedar.eda.sdm)
hct_from_lkg() (scedar.eda.sdm.HClustTree static method)
heatmap() (in module scedar.eda.plot)
hist_dens_plot() (in module scedar.eda.plot)
I
id_x() (scedar.eda.sdm.SampleDistanceMatrix method)
(scedar.eda.sfm.SampleFeatureMatrix method)
(scedar.eda.slcs.SingleLabelClassifiedSamples method)
impute_features() (scedar.knn.imputation.FeatureImputation method)
ind_x() (scedar.eda.sdm.SampleDistanceMatrix method)
(scedar.eda.sfm.SampleFeatureMatrix method)
(scedar.eda.slcs.SingleLabelClassifiedSamples method)
is_uniq_np1darr() (in module scedar.eda.mtype)
is_valid_full_cut_tree_mat() (in module scedar.eda.mtype)
is_valid_lab() (in module scedar.eda.mtype)
is_valid_sfid() (in module scedar.eda.mtype)
K
kde (scedar.eda.mdl.GKdeMdl attribute)
(scedar.eda.mdl.ZeroIGKdeMdl attribute)
kde_mdl (scedar.eda.mdl.ZeroIGKdeMdl attribute)
knn_conn_mat_to_aff_graph() (scedar.eda.sdm.SampleDistanceMatrix static method)
L
lab_mdl() (scedar.eda.slcs.MDLSingleLabelClassifiedSamples method)
lab_sorted_sids() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
lab_x() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
lab_x_bool_inds() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
labs (scedar.cluster.community.Community attribute)
,
[1]
(scedar.cluster.community_mirac.CommunityMIRAC attribute)
,
[1]
(scedar.cluster.mirac.MIRAC attribute)
,
[1]
(scedar.eda.slcs.SingleLabelClassifiedSamples attribute)
labs_to_cmap() (in module scedar.eda.plot)
labs_to_sids() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
leaf_ids() (scedar.eda.sdm.HClustTree method)
left() (scedar.eda.sdm.HClustTree method)
left_count() (scedar.eda.sdm.HClustTree method)
left_leaf_ids() (scedar.eda.sdm.HClustTree method)
load_gz_obj() (in module scedar.utils)
load_obj() (in module scedar.utils)
M
Mdl (class in scedar.eda.mdl)
mdl (scedar.eda.mdl.GKdeMdl attribute)
(scedar.eda.mdl.Mdl attribute)
(scedar.eda.mdl.MultinomialMdl attribute)
(scedar.eda.mdl.ZeroIGKdeMdl attribute)
(scedar.eda.mdl.ZeroIMdl attribute)
(scedar.eda.mdl.ZeroIMultinomialMdl attribute)
MDLSingleLabelClassifiedSamples (class in scedar.eda.slcs)
MDLSingleLabelClassifiedSamples.LabMdlResult (class in scedar.eda.slcs)
merge_labels() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
metric (scedar.eda.sdm.SampleDistanceMatrix attribute)
MIRAC (class in scedar.cluster.mirac)
MultinomialMdl (class in scedar.eda.mdl)
multiple_testing_correction() (in module scedar.eda.stats)
N
n_round_bipar_cnt() (scedar.eda.sdm.HClustTree method)
networkx_graph() (in module scedar.eda.plot)
no_lab_mdl() (scedar.eda.slcs.MDLSingleLabelClassifiedSamples method)
node (scedar.eda.sdm.HClustTree attribute)
np_number_1d() (in module scedar.eda.mdl)
num_correct_dist_mat() (scedar.eda.sdm.SampleDistanceMatrix static method)
P
par_tsne() (scedar.eda.sdm.SampleDistanceMatrix method)
parmap() (in module scedar.utils)
pca_feature_gradient_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
pca_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
per_col_encoders() (scedar.eda.slcs.MDLSingleLabelClassifiedSamples static method)
prev (scedar.eda.sdm.HClustTree attribute)
,
[1]
put_tsne() (scedar.eda.sdm.SampleDistanceMatrix method)
R
RareSampleDetection (class in scedar.knn.detection)
regression_scatter() (in module scedar.eda.plot)
relabel() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
remove_constant_features() (in module scedar.utils)
right() (scedar.eda.sdm.HClustTree method)
right_count() (scedar.eda.sdm.HClustTree method)
right_leaf_ids() (scedar.eda.sdm.HClustTree method)
run() (scedar.cluster.community_mirac.CommunityMIRAC method)
run_community() (scedar.cluster.community_mirac.CommunityMIRAC method)
run_mirac() (scedar.cluster.community_mirac.CommunityMIRAC method)
S
s_cv() (scedar.eda.sfm.SampleFeatureMatrix method)
s_cv_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
s_gc() (scedar.eda.sfm.SampleFeatureMatrix method)
s_gc_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
s_id_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
s_id_regression_scatter() (scedar.eda.sfm.SampleFeatureMatrix method)
s_id_to_ind() (scedar.eda.sfm.SampleFeatureMatrix method)
s_ind_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
s_ind_regression_scatter() (scedar.eda.sfm.SampleFeatureMatrix method)
s_ind_x_pair() (scedar.eda.sfm.SampleFeatureMatrix method)
s_ind_x_vec() (scedar.eda.sfm.SampleFeatureMatrix method)
s_ith_nn_d() (scedar.eda.sdm.SampleDistanceMatrix method)
s_ith_nn_d_dist() (scedar.eda.sdm.SampleDistanceMatrix method)
s_ith_nn_ind() (scedar.eda.sdm.SampleDistanceMatrix method)
s_knn_connectivity_matrix() (scedar.eda.sdm.SampleDistanceMatrix method)
s_knn_graph() (scedar.eda.sdm.SampleDistanceMatrix method)
s_knn_ind_lut() (scedar.eda.sdm.SampleDistanceMatrix method)
s_knns() (scedar.eda.sdm.SampleDistanceMatrix method)
s_n_above_threshold() (scedar.eda.sfm.SampleFeatureMatrix method)
s_n_above_threshold_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
s_sum() (scedar.eda.sfm.SampleFeatureMatrix method)
s_sum_dist() (scedar.eda.sfm.SampleFeatureMatrix method)
SampleDistanceMatrix (class in scedar.eda.sdm)
SampleFeatureMatrix (class in scedar.eda.sfm)
save_obj() (in module scedar.utils)
scedar.cluster.community (module)
scedar.cluster.community_mirac (module)
scedar.cluster.mirac (module)
scedar.eda.mdl (module)
scedar.eda.mtype (module)
scedar.eda.plot (module)
scedar.eda.sdm (module)
scedar.eda.sfm (module)
scedar.eda.slcs (module)
scedar.eda.stats (module)
scedar.knn.detection (module)
scedar.knn.imputation (module)
scedar.utils (module)
select_labs_bool_inds() (scedar.eda.slcs.SingleLabelClassifiedSamples static method)
sids (scedar.eda.sfm.SampleFeatureMatrix attribute)
sids_to_labs() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
SingleLabelClassifiedSamples (class in scedar.eda.slcs)
sort_by_labels() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
sort_features() (scedar.eda.sdm.SampleDistanceMatrix method)
sort_x_by_d() (scedar.eda.sdm.HClustTree static method)
swarm() (in module scedar.eda.plot)
T
to_classified() (scedar.eda.sdm.SampleDistanceMatrix method)
TODO (scedar.cluster.mirac.MIRAC attribute)
tsne() (in module scedar.eda.sdm)
(scedar.eda.sdm.SampleDistanceMatrix method)
tsne_feature_gradient_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
(scedar.eda.slcs.SingleLabelClassifiedSamples method)
tsne_lut (scedar.eda.sdm.SampleDistanceMatrix attribute)
tsne_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
(scedar.eda.slcs.SingleLabelClassifiedSamples method)
tune_mirac() (scedar.cluster.community_mirac.CommunityMIRAC method)
tune_parameters() (scedar.cluster.mirac.MIRAC method)
U
ulab_cnts (scedar.eda.slcs.MDLSingleLabelClassifiedSamples.LabMdlResult attribute)
ulab_mdl_sum (scedar.eda.slcs.MDLSingleLabelClassifiedSamples.LabMdlResult attribute)
ulab_mdls (scedar.eda.slcs.MDLSingleLabelClassifiedSamples.LabMdlResult attribute)
ulab_s_inds (scedar.eda.slcs.MDLSingleLabelClassifiedSamples.LabMdlResult attribute)
umap() (scedar.eda.sdm.SampleDistanceMatrix method)
umap_feature_gradient_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
umap_plot() (scedar.eda.sdm.SampleDistanceMatrix method)
X
x (scedar.eda.mdl.Mdl attribute)
(scedar.eda.sfm.SampleFeatureMatrix attribute)
x_nonzero (scedar.eda.mdl.ZeroIGKdeMdl attribute)
xmat_heatmap() (scedar.eda.slcs.SingleLabelClassifiedSamples method)
Z
ZeroIGKdeMdl (class in scedar.eda.mdl)
ZeroIMdl (class in scedar.eda.mdl)
ZeroIMultinomialMdl (class in scedar.eda.mdl)
zi_mdl (scedar.eda.mdl.ZeroIGKdeMdl attribute)
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