Metacells
latest
README
History
API
Metacells
Index
Edit on GitHub
Index
A
|
B
|
C
|
D
|
E
|
F
|
G
|
H
|
I
|
K
|
L
|
M
|
N
|
O
|
P
|
Q
|
R
|
S
|
T
|
U
|
V
|
W
|
Z
A
allow_inefficient_layout() (in module metacells.utilities.computation)
apply_obs_annotations() (in module metacells.tools.apply)
apply_var_annotations() (in module metacells.tools.apply)
B
bin_fill() (in module metacells.utilities.computation)
bin_pack() (in module metacells.utilities.computation)
bincount_vector() (in module metacells.utilities.computation)
bursty_lonely_downsample_max_cell_quantile (in module metacells.parameters)
bursty_lonely_downsample_min_cell_quantile (in module metacells.parameters)
bursty_lonely_downsample_min_samples (in module metacells.parameters)
bursty_lonely_max_gene_similarity (in module metacells.parameters)
bursty_lonely_max_sampled_cells (in module metacells.parameters)
bursty_lonely_min_gene_normalized_variance (in module metacells.parameters)
bursty_lonely_min_gene_total (in module metacells.parameters)
C
CALC (in module metacells.utilities.logging)
cancel_incrementals() (in module metacells.utilities.logging)
candidates_knn_k_size_factor (in module metacells.parameters)
candidates_max_merge_size_factor (in module metacells.parameters)
candidates_min_split_size_factor (in module metacells.parameters)
cell_umis (in module metacells.parameters)
cells_similarity_log_data (in module metacells.parameters)
cells_similarity_method (in module metacells.parameters)
cells_similarity_value_regularization (in module metacells.parameters)
choose_seeds() (in module metacells.tools.candidates)
collect_metacells() (in module metacells.pipeline.collect)
collect_timing() (in module metacells.utilities.timing)
combine_masks() (in module metacells.tools.mask)
compress_indices() (in module metacells.utilities.computation)
CompressedMatrix (class in metacells.utilities.typing)
compute_candidate_metacells() (in module metacells.tools.candidates)
compute_deviant_folds() (in module metacells.tools.quality)
compute_direct_metacells() (in module metacells.pipeline.direct)
compute_distinct_folds() (in module metacells.tools.distinct)
compute_divide_and_conquer_metacells() (in module metacells.pipeline.divide_and_conquer)
compute_excluded_gene_umis() (in module metacells.tools.properly_sampled)
compute_for_mcview() (in module metacells.pipeline.mcview)
compute_inner_folds() (in module metacells.tools.quality)
compute_knn_by_markers() (in module metacells.pipeline.umap)
compute_obs_obs_knn_graph() (in module metacells.tools.knn_graph)
compute_obs_obs_similarity() (in module metacells.tools.similarity)
compute_outliers_fold_factors() (in module metacells.tools.quality)
compute_outliers_matches() (in module metacells.tools.quality)
compute_projected_folds() (in module metacells.tools.quality)
compute_projected_fractions() (in module metacells.tools.project)
compute_projection_weights() (in module metacells.tools.project)
compute_similar_query_metacells() (in module metacells.tools.quality)
compute_stdev_logs() (in module metacells.tools.quality)
compute_subset_distinct_genes() (in module metacells.tools.distinct)
compute_target_pile_size() (in module metacells.pipeline.divide_and_conquer)
compute_type_genes_normalized_variances() (in module metacells.tools.quality)
compute_umap_by_markers() (in module metacells.pipeline.umap)
compute_var_var_knn_graph() (in module metacells.tools.knn_graph)
compute_var_var_similarity() (in module metacells.tools.similarity)
consider_atlas_noisy_genes (in module metacells.parameters)
consider_query_noisy_genes (in module metacells.parameters)
context (metacells.utilities.timing.StepTiming attribute)
context() (in module metacells.utilities.timing)
convey_atlas_to_query() (in module metacells.tools.project)
convey_group_to_obs() (in module metacells.tools.convey)
convey_obs_fractions_to_group() (in module metacells.tools.convey)
convey_obs_obs_to_group_group() (in module metacells.tools.convey)
convey_obs_to_group() (in module metacells.tools.convey)
convey_obs_to_obs() (in module metacells.tools.convey)
cooldown_node (in module metacells.parameters)
cooldown_pass (in module metacells.parameters)
cooldown_phase (in module metacells.parameters)
copy_adata() (in module metacells.utilities.annotation)
corrcoef() (in module metacells.utilities.computation)
count_significant_inner_folds() (in module metacells.tools.quality)
Counters (class in metacells.utilities.timing)
cover_coordinates() (in module metacells.utilities.computation)
cover_diameter() (in module metacells.utilities.computation)
CPP_DATA_TYPES (in module metacells.utilities.typing)
cpu_ns (metacells.utilities.timing.Counters attribute)
cross_corrcoef_rows() (in module metacells.utilities.computation)
cross_logistics_rows() (in module metacells.utilities.computation)
current_step() (in module metacells.utilities.timing)
D
DefaultValues (class in metacells.tools.apply)
DENSE_FAST_FLAG (in module metacells.utilities.typing)
deviant_cells_regularization_quantile (in module metacells.parameters)
deviants_gap_skip_cells (in module metacells.parameters)
deviants_max_cell_fraction (in module metacells.parameters)
deviants_max_gap_cells_count (in module metacells.parameters)
deviants_max_gap_cells_fraction (in module metacells.parameters)
deviants_max_gene_fraction (in module metacells.parameters)
deviants_min_compare_umis (in module metacells.parameters)
deviants_min_gene_fold_factor (in module metacells.parameters)
deviants_min_noisy_gene_fold_factor (in module metacells.parameters)
deviants_policy (in module metacells.parameters)
did_progress() (in module metacells.utilities.progress)
dissolve_metacells() (in module metacells.tools.dissolve)
dissolve_min_convincing_gene_fold_factor (in module metacells.parameters)
dissolve_min_robust_size_factor (in module metacells.parameters)
distinct_genes_count (in module metacells.parameters)
divide_and_conquer_pipeline() (in module metacells.pipeline.divide_and_conquer)
done_incrementals() (in module metacells.utilities.logging)
downsample_cells() (in module metacells.tools.downsample)
downsample_matrix() (in module metacells.utilities.computation)
downsample_max_cell_quantile (in module metacells.parameters)
downsample_min_cell_quantile (in module metacells.parameters)
downsample_min_samples (in module metacells.parameters)
downsample_vector() (in module metacells.utilities.computation)
E
elapsed_ns (metacells.utilities.timing.Counters attribute)
eliminate_zeros() (in module metacells.utilities.typing)
end_progress_bar() (in module metacells.utilities.progress)
end_progress_bar_slice() (in module metacells.utilities.progress)
exclude_cells() (in module metacells.pipeline.exclude)
exclude_genes() (in module metacells.pipeline.exclude)
expand_doc() (in module metacells.utilities.documentation)
extract_clean_data() (in module metacells.pipeline.exclude)
extract_selected_data() (in module metacells.pipeline.select)
F
filter_data() (in module metacells.tools.filter)
find_bursty_lonely_genes() (in module metacells.tools.bursty_lonely)
find_deviant_cells() (in module metacells.tools.deviants)
find_distinct_genes() (in module metacells.tools.distinct)
find_high_fraction_genes() (in module metacells.tools.high)
find_high_normalized_variance_genes() (in module metacells.tools.high)
find_high_relative_variance_genes() (in module metacells.tools.high)
find_high_topN_genes() (in module metacells.tools.high)
find_high_total_genes() (in module metacells.tools.high)
find_metacells_marker_genes() (in module metacells.tools.high)
find_named_genes() (in module metacells.tools.named)
find_properly_sampled_cells() (in module metacells.tools.properly_sampled)
find_properly_sampled_genes() (in module metacells.tools.properly_sampled)
find_rare_gene_modules() (in module metacells.tools.rare)
flush_timing() (in module metacells.utilities.timing)
fold_description() (in module metacells.utilities.logging)
fraction_by() (in module metacells.utilities.computation)
fraction_description() (in module metacells.utilities.logging)
fraction_of_grouped() (in module metacells.utilities.computation)
fraction_per() (in module metacells.utilities.computation)
fractions_description() (in module metacells.utilities.logging)
freeze() (in module metacells.utilities.typing)
frozen() (in module metacells.utilities.typing)
full (metacells.tools.apply.DefaultValues attribute)
G
geomean_per() (in module metacells.utilities.computation)
get_m_data() (in module metacells.utilities.annotation)
get_max_parallel_piles() (in module metacells.pipeline.divide_and_conquer)
get_name() (in module metacells.utilities.annotation)
get_o_names() (in module metacells.utilities.annotation)
get_o_numpy() (in module metacells.utilities.annotation)
get_o_series() (in module metacells.utilities.annotation)
get_oa_frame() (in module metacells.utilities.annotation)
get_oa_proper() (in module metacells.utilities.annotation)
get_oo_frame() (in module metacells.utilities.annotation)
get_oo_proper() (in module metacells.utilities.annotation)
get_processors_count() (in module metacells.utilities.parallel)
get_v_names() (in module metacells.utilities.annotation)
get_v_numpy() (in module metacells.utilities.annotation)
get_v_series() (in module metacells.utilities.annotation)
get_va_frame() (in module metacells.utilities.annotation)
get_va_proper() (in module metacells.utilities.annotation)
get_vo_frame() (in module metacells.utilities.annotation)
get_vo_proper() (in module metacells.utilities.annotation)
get_vv_frame() (in module metacells.utilities.annotation)
get_vv_proper() (in module metacells.utilities.annotation)
group_obs_annotation() (in module metacells.tools.group)
group_obs_data() (in module metacells.tools.group)
groups_description() (in module metacells.utilities.logging)
groups_similarity_log_data (in module metacells.parameters)
groups_similarity_method (in module metacells.parameters)
guess_max_parallel_piles() (in module metacells.pipeline.divide_and_conquer)
H
has_data() (in module metacells.utilities.annotation)
has_progress_bar() (in module metacells.utilities.progress)
highest_weight() (in module metacells.utilities.computation)
I
ignore_atlas_lateral_genes (in module metacells.parameters)
ignore_query_lateral_genes (in module metacells.parameters)
ImproperMatrix (in module metacells.utilities.typing)
ImproperShaped (in module metacells.utilities.typing)
ImproperVector (in module metacells.utilities.typing)
in_parallel_map() (in module metacells.utilities.timing)
incremental() (in module metacells.utilities.logging)
is_1d() (in module metacells.utilities.typing)
is_2d() (in module metacells.utilities.typing)
is_canonical() (in module metacells.utilities.typing)
is_contiguous() (in module metacells.utilities.typing)
is_layout() (in module metacells.utilities.typing)
is_main_process() (in module metacells.utilities.parallel)
K
knn_balanced_ranks_factor (in module metacells.parameters)
knn_incoming_degree_factor (in module metacells.parameters)
knn_k (in module metacells.parameters)
knn_k_umis_quantile (in module metacells.parameters)
knn_min_outgoing_degree (in module metacells.parameters)
knn_outgoing_degree_factor (in module metacells.parameters)
L
LAYOUT_OF_AXIS (in module metacells.utilities.typing)
log_calc() (in module metacells.utilities.logging)
log_data() (in module metacells.utilities.computation)
log_get() (in module metacells.utilities.logging)
log_return() (in module metacells.utilities.logging)
log_set() (in module metacells.utilities.logging)
log_step() (in module metacells.utilities.logging)
log_steps() (in module metacells.utilities.timing)
logged() (in module metacells.utilities.logging)
logger() (in module metacells.utilities.logging)
logging_calc() (in module metacells.utilities.logging)
logistics() (in module metacells.utilities.computation)
logistics_location (in module metacells.parameters)
logistics_slope (in module metacells.parameters)
M
mark_essential_genes() (in module metacells.pipeline.mark)
mark_ignored_genes() (in module metacells.pipeline.mark)
mark_lateral_genes() (in module metacells.pipeline.mark)
mark_noisy_genes() (in module metacells.pipeline.mark)
mark_select_genes() (in module metacells.pipeline.mark)
markers_knn_min_outgoing_degree (in module metacells.parameters)
mask_description() (in module metacells.utilities.logging)
Matrix (in module metacells.utilities.typing)
matrix_layout() (in module metacells.utilities.typing)
matrix_rows_folds_and_aurocs() (in module metacells.utilities.computation)
max_gbs (in module metacells.parameters)
max_matrix() (in module metacells.utilities.computation)
max_merge_size_factor (in module metacells.parameters)
max_per() (in module metacells.utilities.computation)
max_seed_size_quantile (in module metacells.parameters)
max_split_min_cut_strength (in module metacells.parameters)
max_target_pile_size (in module metacells.parameters)
maybe_compressed_matrix() (in module metacells.utilities.typing)
maybe_numpy_matrix() (in module metacells.utilities.typing)
maybe_numpy_vector() (in module metacells.utilities.typing)
maybe_o_numpy() (in module metacells.utilities.annotation)
maybe_pandas_frame() (in module metacells.utilities.typing)
maybe_pandas_series() (in module metacells.utilities.typing)
maybe_sparse_matrix() (in module metacells.utilities.typing)
maybe_v_numpy() (in module metacells.utilities.annotation)
mean_matrix() (in module metacells.utilities.computation)
mean_per() (in module metacells.utilities.computation)
median_per() (in module metacells.utilities.computation)
metacell_geo_mean (in module metacells.parameters)
metacell_umis_regularization (in module metacells.parameters)
metacells
module
metacells.parameters
module
metacells.pipeline
module
metacells.pipeline.collect
module
metacells.pipeline.direct
module
metacells.pipeline.divide_and_conquer
module
metacells.pipeline.exclude
module
metacells.pipeline.mark
module
metacells.pipeline.mcview
module
metacells.pipeline.projection
module
metacells.pipeline.related_genes
module
metacells.pipeline.select
module
metacells.pipeline.umap
module
metacells.scripts
module
metacells.scripts.timing
module
metacells.tools
module
metacells.tools.apply
module
metacells.tools.bursty_lonely
module
metacells.tools.candidates
module
metacells.tools.convey
module
metacells.tools.deviants
module
metacells.tools.dissolve
module
metacells.tools.distinct
module
metacells.tools.downsample
module
metacells.tools.filter
module
metacells.tools.group
module
metacells.tools.high
module
metacells.tools.knn_graph
module
metacells.tools.layout
module
metacells.tools.mask
module
metacells.tools.named
module
metacells.tools.project
module
metacells.tools.properly_sampled
module
metacells.tools.quality
module
metacells.tools.rare
module
metacells.tools.similarity
module
metacells.utilities
module
metacells.utilities.annotation
module
metacells.utilities.computation
module
metacells.utilities.documentation
module
metacells.utilities.logging
module
metacells.utilities.parallel
module
metacells.utilities.progress
module
metacells.utilities.timing
module
metacells.utilities.typing
module
metacells_gene_range_regularization (in module metacells.parameters)
min_cut() (in module metacells.utilities.computation)
min_cut_seed_cells (in module metacells.parameters)
min_knn_k (in module metacells.parameters)
min_marker_max_metacells_gene_fraction (in module metacells.parameters)
min_marker_metacells_gene_range_fold_factor (in module metacells.parameters)
min_matrix() (in module metacells.utilities.computation)
min_metacell_size (in module metacells.parameters)
min_per() (in module metacells.utilities.computation)
min_robust_size_factor (in module metacells.parameters)
min_seed_size_quantile (in module metacells.parameters)
min_split_size_factor (in module metacells.parameters)
min_target_pile_size (in module metacells.parameters)
misfit_min_metacells_fraction (in module metacells.parameters)
module
metacells
metacells.parameters
metacells.pipeline
metacells.pipeline.collect
metacells.pipeline.direct
metacells.pipeline.divide_and_conquer
metacells.pipeline.exclude
metacells.pipeline.mark
metacells.pipeline.mcview
metacells.pipeline.projection
metacells.pipeline.related_genes
metacells.pipeline.select
metacells.pipeline.umap
metacells.scripts
metacells.scripts.timing
metacells.tools
metacells.tools.apply
metacells.tools.bursty_lonely
metacells.tools.candidates
metacells.tools.convey
metacells.tools.deviants
metacells.tools.dissolve
metacells.tools.distinct
metacells.tools.downsample
metacells.tools.filter
metacells.tools.group
metacells.tools.high
metacells.tools.knn_graph
metacells.tools.layout
metacells.tools.mask
metacells.tools.named
metacells.tools.project
metacells.tools.properly_sampled
metacells.tools.quality
metacells.tools.rare
metacells.tools.similarity
metacells.utilities
metacells.utilities.annotation
metacells.utilities.computation
metacells.utilities.documentation
metacells.utilities.logging
metacells.utilities.parallel
metacells.utilities.progress
metacells.utilities.timing
metacells.utilities.typing
most_frequent() (in module metacells.utilities.computation)
mustbe_canonical() (in module metacells.utilities.typing)
mustbe_compressed_matrix() (in module metacells.utilities.typing)
mustbe_numpy_matrix() (in module metacells.utilities.typing)
mustbe_numpy_vector() (in module metacells.utilities.typing)
mustbe_pandas_frame() (in module metacells.utilities.typing)
mustbe_pandas_series() (in module metacells.utilities.typing)
mustbe_sparse_matrix() (in module metacells.utilities.typing)
N
nanmax_matrix() (in module metacells.utilities.computation)
nanmax_per() (in module metacells.utilities.computation)
nanmean_matrix() (in module metacells.utilities.computation)
nanmean_per() (in module metacells.utilities.computation)
nanmin_matrix() (in module metacells.utilities.computation)
nanmin_per() (in module metacells.utilities.computation)
nanquantile_per() (in module metacells.utilities.computation)
nnz_matrix() (in module metacells.utilities.computation)
nnz_per() (in module metacells.utilities.computation)
normalized_variance_per() (in module metacells.utilities.computation)
now() (metacells.utilities.timing.Counters static method)
NumpyMatrix (in module metacells.utilities.typing)
NumpyVector (in module metacells.utilities.typing)
O
only_atlas_marker_genes (in module metacells.parameters)
only_query_marker_genes (in module metacells.parameters)
optimize_partitions() (in module metacells.tools.candidates)
outliers_fold_regularization (in module metacells.parameters)
outliers_projection_pipeline() (in module metacells.pipeline.projection)
P
pairs_corrcoef_rows() (in module metacells.utilities.computation)
pairs_logistics_rows() (in module metacells.utilities.computation)
PandasFrame (class in metacells.utilities.typing)
PandasSeries (class in metacells.utilities.typing)
parallel_map() (in module metacells.utilities.parallel)
PARAM (in module metacells.utilities.logging)
parameters (metacells.utilities.timing.StepTiming attribute)
parent (metacells.utilities.timing.StepTiming attribute)
patterns_matches() (in module metacells.utilities.computation)
PER_OF_AXIS (in module metacells.utilities.typing)
piles_knn_k_size_factor (in module metacells.parameters)
piles_max_merge_size_factor (in module metacells.parameters)
piles_min_robust_size_factor (in module metacells.parameters)
piles_min_split_size_factor (in module metacells.parameters)
progress_bar() (in module metacells.utilities.progress)
progress_bar_slice() (in module metacells.utilities.progress)
progress_description() (in module metacells.utilities.logging)
project_candidates_count (in module metacells.parameters)
project_corrections (in module metacells.parameters)
project_filter_ranges (in module metacells.parameters)
project_fold_regularization (in module metacells.parameters)
project_ignore_range_min_overlap_fraction (in module metacells.parameters)
project_ignore_range_quantile (in module metacells.parameters)
project_log_data (in module metacells.parameters)
project_max_consistency_fold_factor (in module metacells.parameters)
project_max_projection_fold_factor (in module metacells.parameters)
project_max_projection_noisy_fold_factor (in module metacells.parameters)
project_min_candidates_fraction (in module metacells.parameters)
project_min_corrected_gene_correlation (in module metacells.parameters)
project_min_corrected_gene_factor (in module metacells.parameters)
project_min_query_markers_fraction (in module metacells.parameters)
project_min_significant_gene_umis (in module metacells.parameters)
project_min_usage_weight (in module metacells.parameters)
project_renormalize_query (in module metacells.parameters)
projection_pipeline() (in module metacells.pipeline.projection)
properly_sampled_max_cell_total (in module metacells.parameters)
properly_sampled_max_excluded_genes_fraction (in module metacells.parameters)
properly_sampled_min_cell_total (in module metacells.parameters)
properly_sampled_min_gene_total (in module metacells.parameters)
ProperMatrix (in module metacells.utilities.typing)
ProperShaped (in module metacells.utilities.typing)
prune_per() (in module metacells.utilities.computation)
Q
quality_min_gene_total (in module metacells.parameters)
quantile_per() (in module metacells.utilities.computation)
quick_and_dirty (in module metacells.parameters)
R
Raise (class in metacells.tools.apply)
random_piles() (in module metacells.utilities.computation)
rank_matrix_by_layout() (in module metacells.utilities.computation)
rank_per() (in module metacells.utilities.computation)
rare_deviants_max_cell_fraction (in module metacells.parameters)
rare_dissolve_min_robust_size_factor (in module metacells.parameters)
rare_genes_cluster_method (in module metacells.parameters)
rare_genes_similarity_method (in module metacells.parameters)
rare_max_cells_factor_of_random_pile (in module metacells.parameters)
rare_max_gene_cell_fraction (in module metacells.parameters)
rare_max_genes (in module metacells.parameters)
rare_max_related_gene_increase_factor (in module metacells.parameters)
rare_min_cell_module_total (in module metacells.parameters)
rare_min_cells_of_modules (in module metacells.parameters)
rare_min_convincing_gene_fold_factor (in module metacells.parameters)
rare_min_gene_maximum (in module metacells.parameters)
rare_min_genes_of_modules (in module metacells.parameters)
rare_min_module_correlation (in module metacells.parameters)
rare_min_related_gene_fold_factor (in module metacells.parameters)
ratio_description() (in module metacells.utilities.logging)
relate_to_lateral_genes() (in module metacells.pipeline.related_genes)
related_genes_cluster_method (in module metacells.parameters)
related_genes_similarity_method (in module metacells.parameters)
related_max_genes_of_modules (in module metacells.parameters)
related_max_sampled_cells (in module metacells.parameters)
related_min_gene_correlation (in module metacells.parameters)
related_min_mean_gene_fraction (in module metacells.parameters)
relative_variance_per() (in module metacells.utilities.computation)
relative_variance_window_size (in module metacells.parameters)
represent() (in module metacells.utilities.computation)
S
scale_by() (in module metacells.utilities.computation)
score_partitions() (in module metacells.tools.candidates)
select_downsample_max_cell_quantile (in module metacells.parameters)
select_downsample_min_cell_quantile (in module metacells.parameters)
select_downsample_min_samples (in module metacells.parameters)
select_min_gene_relative_variance (in module metacells.parameters)
select_min_gene_top3 (in module metacells.parameters)
select_min_gene_total (in module metacells.parameters)
select_min_genes (in module metacells.parameters)
set_m_data() (in module metacells.utilities.annotation)
set_max_parallel_piles() (in module metacells.pipeline.divide_and_conquer)
set_name() (in module metacells.utilities.annotation)
set_o_data() (in module metacells.utilities.annotation)
set_oa_data() (in module metacells.utilities.annotation)
set_oo_data() (in module metacells.utilities.annotation)
set_processors_count() (in module metacells.utilities.parallel)
set_v_data() (in module metacells.utilities.annotation)
set_va_data() (in module metacells.utilities.annotation)
set_vo_data() (in module metacells.utilities.annotation)
set_vv_data() (in module metacells.utilities.annotation)
setup_logger() (in module metacells.utilities.logging)
Shaped (in module metacells.utilities.typing)
shaped_checksum() (in module metacells.utilities.typing)
shaped_dtype() (in module metacells.utilities.typing)
shuffle_matrix() (in module metacells.utilities.computation)
significant_gene_fold_factor (in module metacells.parameters)
significant_gene_fraction (in module metacells.parameters)
significant_gene_normalized_variance (in module metacells.parameters)
significant_gene_relative_variance (in module metacells.parameters)
significant_gene_similarity (in module metacells.parameters)
significant_noisy_gene_fold_factor (in module metacells.parameters)
significant_value (in module metacells.parameters)
similarity_method (in module metacells.parameters)
sizes_description() (in module metacells.utilities.logging)
skeleton_k (in module metacells.parameters)
Skip (class in metacells.tools.apply)
slice (metacells.tools.apply.DefaultValues attribute)
slice() (in module metacells.utilities.annotation)
sliding_window_function() (in module metacells.utilities.computation)
sort_compressed_indices() (in module metacells.utilities.computation)
sort_indices() (in module metacells.utilities.typing)
SPARSE_FAST_FORMAT (in module metacells.utilities.typing)
SPARSE_SLOW_FORMAT (in module metacells.utilities.typing)
SparseMatrix (class in metacells.utilities.typing)
sparsify_matrix() (in module metacells.utilities.computation)
spread_coordinates() (in module metacells.tools.layout)
spread_cover_fraction (in module metacells.parameters)
spread_noise_fraction (in module metacells.parameters)
start_progress_bar() (in module metacells.utilities.progress)
start_progress_bar_slice() (in module metacells.utilities.progress)
stdev_per() (in module metacells.utilities.computation)
STEP (in module metacells.utilities.logging)
StepTiming (class in metacells.utilities.timing)
strongest() (in module metacells.utilities.computation)
sum_duplicates() (in module metacells.utilities.typing)
sum_groups() (in module metacells.utilities.computation)
sum_matrix() (in module metacells.utilities.computation)
sum_per() (in module metacells.utilities.computation)
sum_squared_per() (in module metacells.utilities.computation)
T
target_metacell_size (in module metacells.parameters)
target_metacell_umis (in module metacells.parameters)
target_metacells_in_pile (in module metacells.parameters)
thread_name (metacells.utilities.timing.StepTiming attribute)
timed_call() (in module metacells.utilities.timing)
timed_parameters() (in module metacells.utilities.timing)
timed_step() (in module metacells.utilities.timing)
to_contiguous() (in module metacells.utilities.typing)
to_layout() (in module metacells.utilities.computation)
to_numpy_matrix() (in module metacells.utilities.typing)
to_numpy_vector() (in module metacells.utilities.typing)
to_pandas_frame() (in module metacells.utilities.typing)
to_pandas_series() (in module metacells.utilities.typing)
to_proper_matrices() (in module metacells.utilities.typing)
to_proper_matrix() (in module metacells.utilities.typing)
top_level() (in module metacells.utilities.logging)
top_per() (in module metacells.utilities.computation)
total_nested (metacells.utilities.timing.StepTiming attribute)
type_gene_normalized_variance_quantile (in module metacells.parameters)
U
umap_by_distances() (in module metacells.tools.layout)
umap_fraction_regularization (in module metacells.parameters)
umap_ignore_lateral_genes (in module metacells.parameters)
umap_k (in module metacells.parameters)
umap_max_marker_genes (in module metacells.parameters)
umap_min_dist (in module metacells.parameters)
umap_similarity_log_data (in module metacells.parameters)
umap_similarity_method (in module metacells.parameters)
umap_similarity_value_regularization (in module metacells.parameters)
umap_spread (in module metacells.parameters)
unfreeze() (in module metacells.utilities.typing)
unfrozen() (in module metacells.utilities.typing)
V
variance_per() (in module metacells.utilities.computation)
Vector (in module metacells.utilities.typing)
W
weighted_mean() (in module metacells.utilities.computation)
write_projection_weights() (in module metacells.pipeline.projection)
Z
zeros_cell_size_quantile (in module metacells.parameters)
Read the Docs
v: latest
Versions
latest
Downloads
On Read the Docs
Project Home
Builds