APIΒΆ
Metacells single-cell RNA sequencing.
- Pipeline
- Related Genes
relate_to_lateral_genes()
- Exclude
exclude_genes()
exclude_cells()
extract_clean_data()
- Mark (Genes)
mark_lateral_genes()
mark_noisy_genes()
mark_select_genes()
mark_ignored_genes()
mark_essential_genes()
- Selection
extract_selected_data()
- Direct
compute_direct_metacells()
- Divide and Conquer
set_max_parallel_piles()
get_max_parallel_piles()
guess_max_parallel_piles()
compute_target_pile_size()
divide_and_conquer_pipeline()
compute_divide_and_conquer_metacells()
- Collect
collect_metacells()
- UMAP
compute_knn_by_markers()
compute_umap_by_markers()
- Projection
projection_pipeline()
outliers_projection_pipeline()
write_projection_weights()
- MCView
compute_for_mcview()
- Tools
- General Tools
- Filtering the Data
- Filter
filter_data()
- Mask
combine_masks()
- Properly Sampled
compute_excluded_gene_umis()
find_properly_sampled_cells()
find_properly_sampled_genes()
- Named
find_named_genes()
- High
find_high_total_genes()
find_high_topN_genes()
find_high_fraction_genes()
find_high_normalized_variance_genes()
find_high_relative_variance_genes()
find_metacells_marker_genes()
- Noisy Lonely
find_bursty_lonely_genes()
- Rare
find_rare_gene_modules()
- Building the Graph
- Computing the Metacells
- Evaluating the Metacells
- Group
group_obs_data()
group_obs_annotation()
- Quality
compute_stdev_logs()
compute_projected_folds()
compute_similar_query_metacells()
compute_outliers_matches()
compute_deviant_folds()
compute_inner_folds()
compute_type_genes_normalized_variances()
compute_outliers_fold_factors()
count_significant_inner_folds()
compute_distinct_folds()
find_distinct_genes()
compute_subset_distinct_genes()
- Visualizing the Metacells
- Projecting onto Metacells
- Parameters
- Defaults
significant_gene_fraction
significant_gene_normalized_variance
significant_gene_relative_variance
significant_gene_similarity
significant_gene_fold_factor
significant_noisy_gene_fold_factor
significant_value
downsample_min_samples
downsample_min_cell_quantile
downsample_max_cell_quantile
relative_variance_window_size
similarity_method
logistics_location
logistics_slope
min_target_pile_size
max_target_pile_size
target_metacells_in_pile
target_metacell_size
target_metacell_umis
metacell_geo_mean
metacell_umis_regularization
zeros_cell_size_quantile
cell_umis
min_split_size_factor
min_robust_size_factor
max_merge_size_factor
min_metacell_size
max_split_min_cut_strength
min_cut_seed_cells
piles_min_split_size_factor
piles_min_robust_size_factor
piles_max_merge_size_factor
properly_sampled_min_cell_total
properly_sampled_max_cell_total
properly_sampled_min_gene_total
properly_sampled_max_excluded_genes_fraction
related_max_sampled_cells
related_genes_similarity_method
related_genes_cluster_method
related_max_genes_of_modules
related_min_mean_gene_fraction
related_min_gene_correlation
bursty_lonely_max_sampled_cells
bursty_lonely_downsample_min_samples
bursty_lonely_downsample_min_cell_quantile
bursty_lonely_downsample_max_cell_quantile
bursty_lonely_min_gene_total
bursty_lonely_min_gene_normalized_variance
bursty_lonely_max_gene_similarity
rare_max_genes
rare_max_gene_cell_fraction
rare_min_gene_maximum
rare_genes_similarity_method
rare_genes_cluster_method
rare_min_genes_of_modules
rare_min_cells_of_modules
rare_max_cells_factor_of_random_pile
rare_min_module_correlation
rare_min_related_gene_fold_factor
rare_max_related_gene_increase_factor
rare_min_cell_module_total
rare_deviants_max_cell_fraction
quick_and_dirty
select_downsample_min_samples
select_downsample_min_cell_quantile
select_downsample_max_cell_quantile
select_min_gene_relative_variance
select_min_gene_total
select_min_gene_top3
select_min_genes
cells_similarity_log_data
cells_similarity_value_regularization
cells_similarity_method
groups_similarity_log_data
groups_similarity_method
knn_k
candidates_knn_k_size_factor
piles_knn_k_size_factor
knn_k_umis_quantile
min_knn_k
knn_balanced_ranks_factor
knn_incoming_degree_factor
knn_outgoing_degree_factor
knn_min_outgoing_degree
markers_knn_min_outgoing_degree
min_seed_size_quantile
max_seed_size_quantile
cooldown_pass
cooldown_node
cooldown_phase
candidates_min_split_size_factor
candidates_max_merge_size_factor
deviants_policy
deviants_gap_skip_cells
deviants_max_gap_cells_count
deviants_max_gap_cells_fraction
deviant_cells_regularization_quantile
deviants_min_gene_fold_factor
deviants_min_compare_umis
deviants_min_noisy_gene_fold_factor
deviants_max_gene_fraction
deviants_max_cell_fraction
dissolve_min_robust_size_factor
rare_dissolve_min_robust_size_factor
rare_min_convincing_gene_fold_factor
dissolve_min_convincing_gene_fold_factor
distinct_genes_count
umap_max_marker_genes
umap_ignore_lateral_genes
umap_similarity_value_regularization
umap_similarity_log_data
umap_similarity_method
umap_min_dist
umap_spread
umap_k
skeleton_k
umap_fraction_regularization
spread_cover_fraction
spread_noise_fraction
quality_min_gene_total
max_gbs
project_filter_ranges
project_ignore_range_quantile
project_ignore_range_min_overlap_fraction
project_min_query_markers_fraction
project_fold_regularization
project_min_significant_gene_umis
project_candidates_count
project_min_candidates_fraction
project_min_usage_weight
project_max_projection_fold_factor
project_max_projection_noisy_fold_factor
project_max_consistency_fold_factor
project_log_data
outliers_fold_regularization
ignore_atlas_lateral_genes
consider_atlas_noisy_genes
only_atlas_marker_genes
only_query_marker_genes
ignore_query_lateral_genes
consider_query_noisy_genes
misfit_min_metacells_fraction
min_marker_metacells_gene_range_fold_factor
metacells_gene_range_regularization
min_marker_max_metacells_gene_fraction
project_renormalize_query
project_corrections
project_min_corrected_gene_correlation
project_min_corrected_gene_factor
type_gene_normalized_variance_quantile
- Utilities
- Annotation
slice()
copy_adata()
set_name()
get_name()
set_m_data()
get_m_data()
set_o_data()
get_o_series()
get_o_numpy()
get_o_names()
maybe_o_numpy()
set_v_data()
get_v_series()
get_v_numpy()
get_v_names()
maybe_v_numpy()
set_oo_data()
get_oo_frame()
get_oo_proper()
set_vv_data()
get_vv_frame()
get_vv_proper()
set_oa_data()
get_oa_frame()
get_oa_proper()
set_va_data()
get_va_frame()
get_va_proper()
set_vo_data()
get_vo_frame()
get_vo_proper()
has_data()
- Computation
allow_inefficient_layout()
to_layout()
sort_compressed_indices()
corrcoef()
cross_corrcoef_rows()
pairs_corrcoef_rows()
logistics()
cross_logistics_rows()
pairs_logistics_rows()
log_data()
median_per()
mean_per()
nanmean_per()
geomean_per()
max_per()
nanmax_per()
min_per()
nanmin_per()
nnz_per()
sum_per()
sum_squared_per()
rank_per()
top_per()
prune_per()
quantile_per()
nanquantile_per()
scale_by()
fraction_by()
fraction_per()
stdev_per()
variance_per()
normalized_variance_per()
relative_variance_per()
sum_matrix()
nnz_matrix()
mean_matrix()
max_matrix()
min_matrix()
nanmean_matrix()
nanmax_matrix()
nanmin_matrix()
rank_matrix_by_layout()
bincount_vector()
most_frequent()
strongest()
highest_weight()
weighted_mean()
fraction_of_grouped()
downsample_matrix()
downsample_vector()
matrix_rows_folds_and_aurocs()
sliding_window_function()
patterns_matches()
compress_indices()
bin_pack()
bin_fill()
sum_groups()
shuffle_matrix()
cover_diameter()
cover_coordinates()
random_piles()
represent()
min_cut()
sparsify_matrix()
- Typing
CPP_DATA_TYPES
Shaped
ProperShaped
ImproperShaped
Matrix
ProperMatrix
NumpyMatrix
CompressedMatrix
ImproperMatrix
SparseMatrix
PandasFrame
Vector
NumpyVector
ImproperVector
PandasSeries
is_1d()
is_2d()
maybe_numpy_vector()
maybe_numpy_matrix()
maybe_sparse_matrix()
maybe_compressed_matrix()
maybe_pandas_frame()
maybe_pandas_series()
mustbe_numpy_vector()
mustbe_numpy_matrix()
mustbe_sparse_matrix()
mustbe_compressed_matrix()
mustbe_pandas_frame()
mustbe_pandas_series()
to_proper_matrix()
to_proper_matrices()
to_pandas_series()
to_pandas_frame()
frozen()
freeze()
unfreeze()
unfrozen()
to_numpy_matrix()
to_numpy_vector()
DENSE_FAST_FLAG
SPARSE_FAST_FORMAT
SPARSE_SLOW_FORMAT
LAYOUT_OF_AXIS
PER_OF_AXIS
shaped_dtype()
matrix_layout()
is_layout()
is_contiguous()
to_contiguous()
mustbe_canonical()
is_canonical()
eliminate_zeros()
sort_indices()
sum_duplicates()
shaped_checksum()
- Parallel
is_main_process()
set_processors_count()
get_processors_count()
parallel_map()
- Progress
progress_bar()
progress_bar_slice()
did_progress()
has_progress_bar()
start_progress_bar()
end_progress_bar()
start_progress_bar_slice()
end_progress_bar_slice()
- Timing
collect_timing()
flush_timing()
in_parallel_map()
log_steps()
timed_step()
timed_call()
timed_parameters()
context()
current_step()
StepTiming
Counters
- Logging
setup_logger()
logger()
CALC
STEP
PARAM
logged()
top_level()
log_return()
logging_calc()
log_calc()
log_step()
incremental()
done_incrementals()
cancel_incrementals()
log_set()
log_get()
sizes_description()
fractions_description()
groups_description()
mask_description()
ratio_description()
progress_description()
fraction_description()
fold_description()
- Documentation
expand_doc()
- Scripts