List of all items

Structs

• alg::bhc::BhcInput
• alg::bhc::BhcMerge
• alg::cell_pairs::CellPairs
• alg::cell_pairs::PairSet
• alg::collapse_data::CollapsedOut
• alg::collapse_data::CollapsedStat
• alg::collapse_data::ContrastGene
• alg::collapse_data::EmptyArg
• alg::collapse_data::MultilevelCollapseOut
• alg::collapse_data::MultilevelParams
• alg::collapse_data::PbSampleCollection
• alg::collapse_data::PbSampleLayout
• alg::collapse_data::PbTree
• alg::collapse_data::PbTreeParams
• alg::collapse_data::ReassignCellsParams
• alg::collapse_data::RootRecord
• alg::collapse_data::SplitRecord
• alg::collapse_data::StackCollapseOut
• alg::dc_poisson::DcPoissonStats
• alg::dc_poisson::NoGuard
• alg::dc_poisson::Profiles
• alg::dc_poisson::RefineContext
• alg::dc_poisson::RefineParams
• alg::feature_coarsening::FeatureCoarsening
• alg::feature_coarsening::FeatureCoarseningArgs
• alg::feature_coarsening::FeaturePartition
• alg::feature_coarsening::PartitionOptions
• alg::hvg::HvgCliArgs
• alg::hvg::HvgSelection
• alg::hvg::MustTrainFeatures
• alg::nb_dispersion::DispersionTrend
• alg::pseudobulk::CollapsedPseudobulk
• alg::random_projection::MixedPartition
• alg::random_projection::RandColProjOut
• alg::random_projection::RandRowProjOut
• alg::refine_mixed::MixedRefineParams
• alg::refine_multilevel::BbknnProposer
• alg::refine_multilevel::RefineInputs
• alg::refine_multilevel::RefinedAssignment
• alg::retrieval_impute::RetrievalImputeConfig
• alg::union_find::UnionFind
• aux::cell_annotations::CellAnnotations
• aux::cell_annotations::CellTypeMembership
• aux::data_loading::ReadSharedRowsArgs
• aux::data_loading::SparseDataWithBatch
• aux::feature_rows::CountRowMap
• aux::feature_rows::FeatureRow
• aux::frozen_features::FrozenFeatureHost
• aux::frozen_features::FrozenLoadArgs
• aux::gene_sets::GafOpts
• aux::gene_sets::GafRaw
• aux::gene_sets::GeneSets
• aux::gene_sets::Reconciled
• aux::ontology::Ontology
• column_subset::RowMap
• convert::MatrixLayout
• convert::TenxMatrix
• figure::Canvas
• figure::Hist
• figure::Point
• figure::Scatter
• figure::stat::StatData
• figure::term::PlotImage
• interactive::list_tui::Item
• interactive::list_tui::ListView
• interactive::plan_tui::Control
• interactive::plan_tui::Plan
• interactive::plan_tui::PlanView
• interactive::qc_tui::QcView
• interactive::stat_tui::Dataset
• interactive::stat_tui::Picked
• interactive::stat_tui::StatExplorer
• interactive::stat_tui::Values
• interactive::ui::Binned
• interactive::ui::Binning
• interactive::ui::HistPlot
• interactive::ui::MirrorPlot
• interactive::ui::MirrorSide
• interactive::ui::Tui
• qc::SqueezeCutoffs
• qc::axis::Axis
• qc_lib::QcArgs
• qc_lib::QcConfig
• qc_lib::QcMetrics
• qc_lib::QcReport
• qc_lib::RobustBand
• qc_lib::Verdicts
• qc_rules::CellRules
• qc_rules::RuleCount
• sparse_backend::zarr::SparseMtxData
• sparse_io::CscMatrix
• sparse_io::CsrMatrix
• sparse_io::PreloadReservation
• sparse_io::Tensor
• sparse_io_stack::SparseIoStack
• sparse_io_vector::BackendLocation
• sparse_io_vector::SparseIoVec
• sparse_io_vector::TripletsMatched
• sparse_io_vector::scales::ColumnScales
• sparse_util::CooTripletsShape
• sparse_util::TripletsShape
• sparse_util::ValuesIndicesPointers
• utilities::name_matching::GeneIndex
• utilities::name_matching::RowTypeFilter
• zarr_io::OutputTarget

Enums

• alg::collapse_data::BelowEdge
• alg::dc_poisson::FeatureWeighting
• alg::dc_poisson::ProfileSource
• aux::feature_names::FeatureNameKind
• aux::feature_names::FeatureNameKindArg
• aux::feature_rows::UnparsedRowPolicy
• aux::ontology::Rel
• figure::Anchor
• figure::qc::Panel
• interactive::plan_tui::Setting
• interactive::qc_tui::Decision
• interactive::stat_tui::Purpose
• interactive::stat_tui::Side
• interactive::ui::Scale
• qc_lib::Tail
• qc_rules::Mode
• qc_rules::Rule
• sparse_io::CsKey
• sparse_io::SparseIoBackend
• sparse_io_vector::ColumnAlignment
• sparse_io_vector::RowAlignment
• sparse_io_vector::scales::RowFilter
• sparse_util::IndexPointerType

Traits

• alg::collapse_data::CollapsingOps
• alg::collapse_data::MultilevelCollapsingOps
• alg::dc_poisson::CandidateProposer
• alg::dc_poisson::MoveGuard
• alg::normalization::NormalizeDistance
• alg::random_projection::RandProjOps
• alg::refine_mixed::MixedRefineOps
• interactive::ui::BarValue
• interactive::ui::Screen
• sparse_data_visitors::VisitColumnsOps
• sparse_io::SparseIo
• sparse_util::SparseTripletsTraits

Macros

• sparse_io::array
• sparse_io::azip
• sparse_io::s

Functions

• alg::batch_mixing::batch_indices
• alg::batch_mixing::centre_batches_within_state
• alg::batch_mixing::default_state_bits
• alg::batch_mixing::merge_poorly_mixed_bins
• alg::bhc::bhc_cut
• alg::bhc::bhc_cut_with_sizes
• alg::bhc::bhc_merge
• alg::cell_pairs::collapse_pairs
• alg::collapse_data::collapse_columns_multilevel_with_hierarchy
• alg::collapse_data::collapse_columns_multilevel_with_partition
• alg::collapse_data::collapse_columns_multilevel_with_strata
• alg::collapse_data::collapse_stack_multilevel_with_hierarchy
• alg::collapse_data::resample_and_optimize
• alg::dc_poisson::argmax_log_restricted
• alg::dc_poisson::argmax_log_restricted_from
• alg::dc_poisson::compact_labels
• alg::dc_poisson::compute_log_probs_restricted
• alg::dc_poisson::compute_sibling_sets
• alg::dc_poisson::intersect_with_siblings_fallback
• alg::dc_poisson::refine_with_candidates
• alg::dc_poisson::refine_with_candidates_guarded
• alg::dc_poisson::refine_with_proposer
• alg::dc_poisson::refine_with_proposer_guarded
• alg::dc_poisson::sample_categorical_log_restricted
• alg::feature_coarsening::coarsen_features
• alg::feature_coarsening::informative_features
• alg::feature_coarsening::partition_features
• alg::gene_weighting::apply_gene_weights
• alg::gene_weighting::compute_nb_fisher_weights
• alg::gene_weighting::compute_nb_fisher_weights_coarsened
• alg::gene_weighting::fisher_weights_from_pseudobulk
• alg::gene_weighting::fisher_weights_from_stats
• alg::gene_weighting::load_fisher_weights
• alg::gene_weighting::load_fisher_weights_coarse
• alg::gene_weighting::load_per_gene_weights
• alg::gene_weighting::save_fisher_weights
• alg::gene_weighting::save_fisher_weights_coarse
• alg::gene_weighting::save_per_gene_weights
• alg::hvg::load_must_train
• alg::hvg::load_must_train_union
• alg::hvg::select_hvg
• alg::hvg::select_hvg_by_stats
• alg::hvg::select_hvg_streaming
• alg::hvg::select_hvg_with_indices
• alg::hvg::union_indices
• alg::pseudobulk::collapse_pseudobulk
• alg::pseudobulk::collapse_pseudobulk_weighted
• alg::random_projection::binary_sort_columns
• alg::random_projection::max_binary_code
• alg::random_projection::mixed_partition
• alg::refine_multilevel::refine_assignments
• alg::retrieval_impute::retrieval_impute
• alg::sparse_streaming::streaming_sparse_running_stats
• alg::sparse_streaming::streaming_sparse_running_stats_folded
• aux::cell_annotations::build_onehot_membership
• aux::cell_annotations::infer_cell_annotations
• aux::cell_annotations::read_cell_annotations
• aux::cell_annotations::read_membership_proportions
• aux::data_loading::read_data_on_shared_rows
• aux::feature_names::build_locus_overlap_canonical_map
• aux::feature_names::build_locus_overlap_canonicalizer
• aux::feature_names::build_mixed_kind_canonicalizer
• aux::feature_names::locus_key
• aux::feature_names::parse_locus
• aux::feature_rows::channels
• aux::feature_rows::feature_row
• aux::feature_rows::intern_count_rows
• aux::feature_rows::parse_feature_row
• aux::feature_rows::split_count_row
• aux::feature_rows::unit_row
• aux::feature_types::feature_rows
• aux::feature_types::feature_types_path
• aux::feature_types::is_data_feature_type
• aux::feature_types::read_feature_types
• aux::feature_types::write_feature_types
• aux::frozen_features::load_frozen_feature_host
• aux::frozen_features::load_frozen_feature_host_matching
• aux::gene_sets::membership_rows
• aux::gene_sets::read_gaf
• aux::gene_sets::read_gaf_without_evidence
• aux::gene_sets::read_gmt
• aux::gene_sets::read_membership_pairs
• column_subset::stream_column_selection
• column_subset::stream_mapped_selection
• convert::build_from_zarr_matrix
• convert::convert_zarr_to_backend
• convert::try_open_or_convert
• convert::write_10x_matrix
• figure::bins_for
• figure::esc
• figure::free_name
• figure::image
• figure::plot_area
• figure::png
• figure::qc::draw_panel
• figure::qc::edge_text
• figure::qc::figure
• figure::qc::panel
• figure::qc::panels
• figure::qc::shown
• figure::ramp
• figure::save
• figure::saved_paths
• figure::short
• figure::stat::draw_mean_sd
• figure::stat::draw_stat
• figure::stat::figure
• figure::taken
• figure::term::picker
• figure::text_width
• hdf5_io::resolve_backend_file
• hdf5_io::strip_backend_suffix
• interactive::list_tui::browse_in
• interactive::opens_view
• interactive::picks
• interactive::plan_tui::plan_in
• interactive::qc_tui::choose_rules
• interactive::qc_tui::free_output
• interactive::qc_tui::output_taken
• interactive::qc_tui::shell_word
• interactive::qc_tui::stem
• interactive::session_help
• interactive::session_keys
• interactive::stat_tui::explore
• interactive::stat_tui::explore_in
• interactive::tui_available
• interactive::ui::compact
• interactive::ui::copy
• interactive::ui::header
• interactive::ui::help_line
• interactive::ui::input_line
• interactive::ui::median
• interactive::ui::modes_of
• interactive::ui::notify
• interactive::ui::panel
• interactive::ui::run_screen
• interactive::ui::run_screen_in
• interactive::ui::run_screen_in_with
• interactive::ui::run_screen_with
• interactive::ui::title_bar
• logging::init_logger
• logging::new_progress_bar
• logging::new_spinner
• qc::below_nnz_cutoff
• qc::collect_column_row_stat
• qc::collect_column_stat
• qc::collect_column_stat_across_vec
• qc::collect_row_stat
• qc::collect_row_stat_across_vec
• qc::collect_stratified_row_stat_across_vec
• qc::eprint_nnz_summary
• qc::fmt_stat
• qc::masked_column_stat
• qc::median_of_sorted
• qc::pct
• qc::print_nnz_summary
• qc::squeeze_by_nnz
• qc::suggest_nnz_cutoff
• qc::write_nnz_summary
• qc_lib::cell_verdicts
• qc_lib::compute_qc
• qc_lib::compute_qc_exempting
• qc_lib::compute_qc_metrics
• qc_lib::compute_qc_stack
• qc_lib::filter_by_keep
• qc_lib::qc_report
• qc_lib::resolve_rows_by_regex
• qc_lib::robust_band
• qc_lib::robust_outlier_keep
• qc_lib::write_qc_report
• sparse_data_visitors::create_jobs
• sparse_data_visitors::styled_progress_bar
• sparse_io::auto_preload_enabled
• sparse_io::build_name2index_map
• sparse_io::create_sparse_from_dmatrix
• sparse_io::create_sparse_from_mtx_file
• sparse_io::create_sparse_from_ndarray
• sparse_io::create_sparse_from_triplets
• sparse_io::create_sparse_from_triplets_owned
• sparse_io::create_sparse_streaming_empty
• sparse_io::dmatrix_to_triplets
• sparse_io::meta::common_metadata
• sparse_io::ndarray_to_triplets
• sparse_io::open_sparse_matrix
• sparse_io::open_sparse_matrix_by_path
• sparse_io::preload_reserved_bytes
• sparse_io::preload_within_budget
• sparse_io::remove_backend_path
• sparse_io::reserve_preload
• sparse_io::sparse_io_box_to_arc
• utilities::io_helpers::chunk_elems
• utilities::io_helpers::index_count
• utilities::io_helpers::index_ranges
• utilities::io_helpers::parse_index_spec
• utilities::io_helpers::parse_index_spec_within
• utilities::io_helpers::parse_name_file
• utilities::io_helpers::read_col_names
• utilities::io_helpers::read_row_names
• utilities::name_matching::colon_peak_names
• utilities::name_matching::compose_id_name
• utilities::name_matching::contains_ignore_ascii_case
• utilities::name_matching::filter_row_indices_by_type
• utilities::name_matching::flexible_name_match
• utilities::name_matching::id_name
• utilities::name_matching::idf_weight
• utilities::name_matching::make_names_unique
• utilities::name_matching::match_by_substring
• utilities::name_matching::names_matching
• utilities::name_matching::split_id_name
• zarr_io::apply_zip_flag
• zarr_io::extract_zarr_zip
• zarr_io::finalize_output
• zarr_io::finalize_zarr_output
• zarr_io::in_stage
• zarr_io::leave_stage
• zarr_io::make_stage
• zarr_io::materialize_writable_backend
• zarr_io::open_zarr_store
• zarr_io::open_zarr_store_rw
• zarr_io::output_path
• zarr_io::output_target
• zarr_io::parse_10x_cell_id
• zarr_io::parse_10x_cell_id_flat
• zarr_io::prepare_output
• zarr_io::read_zarr_array_attr
• zarr_io::read_zarr_coordinates
• zarr_io::read_zarr_flat_f32
• zarr_io::read_zarr_flat_u32
• zarr_io::read_zarr_group_attr
• zarr_io::read_zarr_matrix
• zarr_io::read_zarr_ndarray
• zarr_io::read_zarr_numerics
• zarr_io::read_zarr_strings
• zarr_io::staging_zarr_dir

Type Aliases

• alg::collapse_data::GeneSums
• alg::gene_weighting::GeneWeights
• aux::feature_types::FeatureType
• aux::frozen_features::SourceNameMap
• interactive::plan_tui::Planner
• interactive::stat_tui::Loader
• interactive::stat_tui::ValuesReader
• sparse_io::DMatrix
• sparse_io::meta::Metadata
• sparse_io_vector::ColumnNameCanonicalizer
• sparse_io_vector::RowNameCanonicalizer
• zarr_io::ZarrStoreRw

Statics

• logging::MULTI_PROGRESS

Constants

• alg::batch_mixing::CENTRING_ROUNDS
• alg::batch_mixing::DEFAULT_MERGE_LEVELS
• alg::batch_mixing::DEFAULT_MIN_BATCHES_PER_GROUP
• alg::batch_mixing::MAX_STATE_BITS
• alg::collapse_data::DEFAULT_KNN
• alg::collapse_data::DEFAULT_OPT_ITER
• alg::dc_poisson::BATCH_FACTOR_BOUND
• alg::dc_poisson::BATCH_FACTOR_PSEUDO_COUNT
• alg::dc_poisson::LOG_EPS
• alg::random_projection::DEFAULT_PROJECTION_SEED
• aux::feature_rows::ALT
• aux::feature_rows::APA
• aux::feature_rows::ATOI
• aux::feature_rows::BAF
• aux::feature_rows::COUNT
• aux::feature_rows::DEPTH
• aux::feature_rows::DISTAL
• aux::feature_rows::EDITED
• aux::feature_rows::M6A
• aux::feature_rows::METHYLATED
• aux::feature_rows::NO_GENE
• aux::feature_rows::PROXIMAL
• aux::feature_rows::SPLICED
• aux::feature_rows::TOTAL
• aux::feature_rows::UNEDITED
• aux::feature_rows::UNMETHYLATED
• aux::feature_rows::UNSPLICED
• aux::feature_types::GENE_TYPE
• aux::feature_types::REGION_TYPE
• aux::feature_types::TERM_TYPE
• aux::feature_types::WORD_TYPE
• aux::gene_sets::COVERAGE_WARN_FRAC
• aux::gene_sets::UNSUPPORTED_EVIDENCE
• figure::ACCENT
• figure::BAR
• figure::FAINT
• figure::GRID
• figure::INK
• figure::MUTED
• figure::stat::STATS
• interactive::BATCH_ENV
• interactive::TOOL
• interactive::ui::ACCENT
• interactive::ui::ACCENTED
• interactive::ui::DIM
• interactive::ui::HIGHLIGHT
• interactive::ui::PLAIN
• interactive::ui::TICK
• sparse_io::COLUMN_SEP
• sparse_io::MAX_COLUMN_NAME_IDX
• sparse_io::MAX_ROW_NAME_IDX
• sparse_io::ROW_SEP
• sparse_io::SLAB_BUDGET_BYTES
• sparse_io::TRIPLET_BYTES
• sparse_io::meta::CONTENT
• sparse_io::meta::GENE_COUNT
• sparse_io::meta::PRODUCER
• sparse_io::meta::SAMPLE