Index

_

_active_coef_idx_list (adobo.glm.glmnet.ElasticNet attribute) _active_coefs (adobo.glm.glmnet.ElasticNet attribute) _assays (adobo.data.dataset attribute)

_j_to_active_map (adobo.glm.glmnet.ElasticNet attribute) _low_quality_cells (adobo.data.dataset attribute) _norm_data (adobo.data.dataset attribute)

A

add_meta_data() (adobo.data.dataset method) adobo.bio (module) adobo.clustering (module) adobo.data (module) adobo.dr (module) adobo.glm (module) adobo.glm.families (module) adobo.glm.glm (module) adobo.glm.glmnet (module) adobo.glm.simulation (module)

adobo.glm.utils (module) adobo.hvg (module) adobo.irlbpy (module) adobo.irlbpy.irlb (module) adobo.normalize (module) adobo.plotting (module) adobo.preproc (module) adobo.traj (module) alpha (adobo.glm.glm.GLM attribute) assays() (adobo.data.dataset method)

B

Bernoulli (class in adobo.glm.families)

brennecke() (in module adobo.hvg)

C

cell_cycle_predict() (in module adobo.bio) cell_cycle_train() (in module adobo.bio) cell_type_predict() (in module adobo.bio) cell_viz() (in module adobo.plotting) check_commensurate() (in module adobo.glm.utils) check_intercept() (in module adobo.glm.utils) check_offset() (in module adobo.glm.utils) check_sample_weights() (in module adobo.glm.utils) check_types() (in module adobo.glm.utils)

chen2016() (in module adobo.hvg) clean_matrix() (in module adobo.normalize) clone() (adobo.glm.glm.GLM method) clr() (in module adobo.normalize) coef_ (adobo.glm.glm.GLM attribute) coef_() (adobo.glm.glmnet.ElasticNet property) coef_covariance_matrix_() (adobo.glm.glm.GLM property) coef_standard_error_() (adobo.glm.glm.GLM property) ComBat() (in module adobo.normalize) count_data (adobo.data.dataset attribute)

D

d_inv_link() (adobo.glm.families.Bernoulli method) (adobo.glm.families.ExponentialFamily method) (adobo.glm.families.Gamma method) (adobo.glm.families.Gaussian method) (adobo.glm.families.QuasiPoisson method) dataset (class in adobo.data) default_X_names() (in module adobo.glm.utils) default_y_name() (in module adobo.glm.utils) delete() (adobo.data.dataset method)

desc (adobo.data.dataset attribute) deviance() (adobo.glm.families.Bernoulli method) (adobo.glm.families.ExponentialFamily method) (adobo.glm.families.Gamma method) (adobo.glm.families.Gaussian method) (adobo.glm.families.QuasiPoisson method) deviance_ (adobo.glm.glm.GLM attribute) df_mem_usage() (adobo.data.dataset method) dispersion_() (adobo.glm.glm.GLM property)

E

ElasticNet (class in adobo.glm.glmnet) exp_genes() (in module adobo.plotting)

Exponential (class in adobo.glm.families) ExponentialFamily (class in adobo.glm.families) ExponentialFamilyMixin (class in adobo.glm.families)

F

family (adobo.glm.glm.GLM attribute) find_ercc() (in module adobo.preproc) find_hvg() (in module adobo.hvg) find_low_quality_cells() (in module adobo.preproc) find_mitochondrial_genes() (in module adobo.preproc)

fit() (adobo.glm.glm.GLM method) (adobo.glm.glmnet.ElasticNet method) (adobo.glm.glmnet.GLMNet method) force_graph() (in module adobo.dr) formula (adobo.glm.glm.GLM attribute) fqn() (in module adobo.normalize)

G

Gamma (class in adobo.glm.families) Gaussian (class in adobo.glm.families) generate() (in module adobo.clustering) genes2scores() (in module adobo.dr)

genes_violin() (in module adobo.plotting) get_assay() (adobo.data.dataset method) GLM (class in adobo.glm.glm) GLMNet (class in adobo.glm.glmnet)

H

has_converged() (in module adobo.glm.utils) has_dispersion (adobo.glm.families.Bernoulli attribute) (adobo.glm.families.Exponential attribute) (adobo.glm.families.Gamma attribute) (adobo.glm.families.Gaussian attribute) (adobo.glm.families.Poisson attribute) (adobo.glm.families.QuasiPoisson attribute)

has_intercept_column() (in module adobo.glm.utils) has_same_length() (in module adobo.glm.utils)

I

identity_link() (adobo.glm.families.Gamma method) igraph() (in module adobo.clustering) imp_count_data (adobo.data.dataset attribute) impute() (in module adobo.preproc) information_matrix_ (adobo.glm.glm.GLM attribute) initial_working_response() (adobo.glm.families.Bernoulli method) (adobo.glm.families.Gaussian method) initial_working_weights() (adobo.glm.families.Bernoulli method) (adobo.glm.families.Gaussian method)

intercept_ (adobo.glm.glmnet.ElasticNet attribute) inv_link() (adobo.glm.families.Bernoulli method) (adobo.glm.families.ExponentialFamily method) (adobo.glm.families.Gamma method) (adobo.glm.families.Gaussian method) (adobo.glm.families.QuasiPoisson method) invcheck() (in module adobo.irlbpy.irlb) irlb() (in module adobo.dr) is_commensurate() (in module adobo.glm.utils) is_normalized() (adobo.data.dataset method)

J

jackstraw() (in module adobo.dr)

jackstraw_barplot() (in module adobo.plotting)

K

knn() (in module adobo.clustering)

L

lanczos() (in module adobo.irlbpy.irlb) LanczosResult (class in adobo.irlbpy.irlb)

leiden() (in module adobo.clustering) louvain() (in module adobo.clustering) low_quality_cells() (adobo.data.dataset property)

M

mad_outlier() (in module adobo.preproc) make_working_response_and_weights() (adobo.glm.glmnet.GLMNet method) MatrixShapeException meta_cells (adobo.data.dataset attribute)

meta_genes (adobo.data.dataset attribute) mm() (in module adobo.hvg) multA() (in module adobo.irlbpy.irlb) multS() (in module adobo.irlbpy.irlb)

N

n (adobo.glm.glm.GLM attribute) (adobo.glm.glmnet.ElasticNet attribute)

non_parametric_bootstrap() (adobo.glm.simulation.Simulation method) norm() (in module adobo.normalize) norm_data() (adobo.data.dataset property)

O

orthog() (in module adobo.irlbpy.irlb) output_file (adobo.data.dataset attribute)

overall() (in module adobo.plotting) overall_scatter() (in module adobo.plotting)

P

p (adobo.glm.glm.GLM attribute) (adobo.glm.glmnet.ElasticNet attribute) p_values_() (adobo.glm.glm.GLM property) parametric_bootstrap() (adobo.glm.simulation.Simulation method) pca() (in module adobo.dr) pca_contributors() (in module adobo.plotting) pca_elbow() (in module adobo.plotting)

penalized_deviance() (adobo.glm.families.ExponentialFamilyMixin method) Poisson (class in adobo.glm.families) predict() (adobo.glm.glm.GLM method) (adobo.glm.glmnet.ElasticNet method) prepare_s() (in module adobo.irlbpy.irlb) prepare_v() (in module adobo.irlbpy.irlb) print_dict() (adobo.data.dataset method)

Q

QuasiPoisson (class in adobo.glm.families)

R

regress() (in module adobo.dr)

reset_filters() (in module adobo.preproc) rpkm() (in module adobo.normalize)

S

sample() (adobo.glm.families.Bernoulli method) (adobo.glm.families.ExponentialFamily method) (adobo.glm.families.Gamma method) (adobo.glm.families.Gaussian method) (adobo.glm.families.QuasiPoisson method) (adobo.glm.simulation.Simulation method) save() (adobo.data.dataset method) score() (adobo.glm.glm.GLM method) scran() (in module adobo.hvg) set_assay() (adobo.data.dataset method)

seurat() (in module adobo.hvg) simple_filter() (in module adobo.preproc) Simulation (class in adobo.glm.simulation) slingshot() (in module adobo.traj) snn() (in module adobo.clustering) soft_threshold() (in module adobo.glm.utils) sparse (adobo.data.dataset attribute) standard() (in module adobo.normalize) summary() (adobo.glm.glm.GLM method) svd() (in module adobo.dr) symbol_switch() (in module adobo.preproc)

T

tree() (in module adobo.plotting)

tsne() (in module adobo.dr)

U

umap() (in module adobo.dr)

V

variance() (adobo.glm.families.Bernoulli method) (adobo.glm.families.ExponentialFamily method) (adobo.glm.families.Gamma method) (adobo.glm.families.Gaussian method) (adobo.glm.families.QuasiPoisson method)

VectorLengthException version (adobo.data.dataset attribute) vsn() (in module adobo.normalize)

W

weighted_column_dots() (in module adobo.glm.utils)

weighted_dot() (in module adobo.glm.utils) weighted_means() (in module adobo.glm.utils)

X

X_info (adobo.glm.glm.GLM attribute)

X_names (adobo.glm.glm.GLM attribute)

Y

y_names (adobo.glm.glm.GLM attribute)