List of all items

Structs

• enrichment::blitzgsea::BlitzGseaNull
• enrichment::blitzgsea::BlitzGseaParams
• enrichment::blitzgsea::BlitzGseaResults
• enrichment::blitzgsea::BlitzGseaTail
• enrichment::gsea::GseaBatchResults
• enrichment::gsea::GseaParams
• enrichment::gsea::GseaResults
• enrichment::gsea::GseaStats
• enrichment::gsea::SegmentTree
• enrichment::mitch::MitchResult
• enrichment::mitch::MitchTotals
• enrichment::oae::HypergeomResult
• enrichment::singscore::SingscoreMultiResult
• enrichment::singscore::SingscorePermutationResult
• enrichment::singscore::SingscoreSingleResult
• graph::graph_abstraction::PartitionConnectivity
• graph::graph_label_propagations::KnnLabPropGraph
• graph::graph_structures::AttributedGraph
• graph::graph_structures::CoarseLevel
• graph::graph_structures::GraphHierarchy
• graph::graph_structures::SparseGraph
• graph::graph_structures::UnionFind
• graph::leiden::LeidenParams
• graph::page_rank::ConstrainedPageRankGraph
• graph::page_rank::ConstrainedPageRankWorkingMemory
• graph::page_rank::PageRankGraph
• graph::page_rank::PageRankWorkingMemory
• methods::cis_target::MotifEnrichment
• methods::dgrdl::Dgrdl
• methods::dgrdl::DgrdlCache
• methods::dgrdl::DgrdlObjectives
• methods::dgrdl::DgrdlParams
• methods::dgrdl::DgrdlResults
• methods::diffcor::DiffCorRes
• methods::ica::IcaCvData
• methods::ica::IcaParams
• methods::lda::LdaCorpus
• methods::lda::LdaParams
• methods::lda::LdaResult
• methods::lda::LdaSweepEntry
• methods::lda::LdaSweepResult
• methods::lda::metrics::LdaMetrics
• methods::multi_cca::MultiCcaParams
• methods::multi_cca::MultiCcaPermuteParams
• methods::multi_cca::MultiCcaPermuteResult
• methods::multi_cca::MultiCcaResult
• methods::nmf_hals::HalsOpts
• methods::nmf_hals::NmfResult
• methods::nmf_hals::StabilisedNmfResult
• methods::nmf_hals::consensus::ConsensusClusters
• methods::nmf_hals::consensus::ConsensusNmfResult
• methods::nmf_hals::consensus::ConsensusParams
• methods::nmf_hals::consensus::KSweepEntry
• methods::nmf_hals::dense::DenseInput
• methods::nmf_hals::sparse::SparseInput
• methods::rbh::RbhResult
• methods::rbh::RbhTripletStruc
• ontology::go_elim::GeneOntology
• ontology::go_elim::GeneOntologyRandomPerm
• ontology::go_elim::GoElimFinalResults
• ontology::go_elim::GoElimLevelResults
• ontology::go_elim::GoElimLevelResultsGsea
• ontology::similarity::OntoSimRes
• ontology::similarity::WangSimOntology
• prelude::CompressedSparseData2
• prelude::LanczosParams
• prelude::RevOrderedFloat
• prelude::SparseAxis

Enums

• enrichment::gsva::GsvaKernel
• enrichment::singscore::SingscoreRankType
• errors::MethodsErrors
• graph::graph_label_propagations::SymmetryWeightStrategy
• graph::knn_graph::KnnSymmetrisation
• graph::knn_graph::SnnSimilarity
• graph::leiden::LocalMoving
• methods::cis_target::RccType
• methods::graph_diffusions::TiedSumType
• methods::ica::IcaType
• methods::lda::LdaLearning
• methods::nmf_hals::NmfInit
• methods::nmf_hals::consensus::ConsensusTarget
• methods::nmf_hals::nmf_preprocessing::NmfPreprocessing
• prelude::CompressedSparseFormat
• prelude::CoreErrors
• prelude::Verbosity

Traits

• graph::leiden::LocalMover
• methods::nmf_hals::NmfInput
• prelude::BixverseFloat
• prelude::BixverseNumeric
• prelude::BixverseSimd
• prelude::VecConvert
• prelude::VecFloatConvert
• prelude::VecIndexCast

Macros

• prelude::assert_nrows
• prelude::assert_same_len
• prelude::assert_symmetric_mat

Functions

• enrichment::blitzgsea::blitzgsea_score
• enrichment::blitzgsea::calibrate_null
• enrichment::blitzgsea::pval_and_nes
• enrichment::gsea::calc_gsea_stat_cumulative
• enrichment::gsea::calc_gsea_stat_cumulative_batch
• enrichment::gsea::calc_gsea_stat_traditional_batch
• enrichment::gsea::calc_gsea_stats
• enrichment::gsea::calc_gsea_stats_wrapper
• enrichment::gsea::calc_simple_and_multi_error
• enrichment::gsea::calculate_es
• enrichment::gsea::calculate_nes_es_pval
• enrichment::gsea::create_perm_es_simple
• enrichment::gsea::create_random_gs_indices
• enrichment::gsea::fgsea_multilevel_helper
• enrichment::gsea::fgsea_order
• enrichment::gsea::ranks_from_order
• enrichment::gsva::gsva
• enrichment::gsva::gsva_score_genesets
• enrichment::gsva::matrix_kernel_density
• enrichment::gsva::order_rankstat
• enrichment::gsva::parse_gsva_kernel
• enrichment::gsva::ssgsea
• enrichment::mitch::manova_mitch
• enrichment::mitch::manova_mitch_cached
• enrichment::mitch::mitch_rank
• enrichment::mitch::process_mitch_pathway
• enrichment::mitch::process_mitch_pathway_cached
• enrichment::oae::count_hits
• enrichment::oae::filter_gse_results
• enrichment::oae::hypergeom_helper
• enrichment::oae::hypergeom_odds_ratio
• enrichment::singscore::rank_matrix_col_stable
• enrichment::singscore::singscore_multi
• enrichment::singscore::singscore_permutation_test
• enrichment::singscore::singscore_single
• graph::community_detections::walktrap_sparse_graph
• graph::graph_abstraction::partition_connectivities
• graph::graph_clustering::spectral_clustering
• graph::graph_components::connected_components
• graph::graph_components::induced_components
• graph::graph_label_propagations::parse_symmetry_strategy
• graph::graph_metrics::conductance_undirected
• graph::graph_structures::adjacency_to_laplacian
• graph::graph_structures::edge_pairs_to_sparse_graph
• graph::graph_structures::get_knn_graph_adj
• graph::graph_structures::graph_from_strings_with_attributes
• graph::knn_graph::build_knn_graph
• graph::knn_graph::flatten_knn
• graph::knn_graph::parse_snn_similarity
• graph::leiden::community_detection
• graph::leiden::community_detection_with
• graph::leiden::leiden_sparse_graph
• graph::leiden::louvain_sparse_graph
• graph::leiden::modularity
• graph::leiden::parse_local_moving
• graph::page_rank::constrained_personalised_page_rank
• graph::page_rank::constrained_personalised_page_rank_optimised
• graph::page_rank::personalised_page_rank
• graph::page_rank::personalised_page_rank_optimised
• graph::shortest_paths::dijkstra_from_source
• graph::shortest_paths::multi_source_dijkstra
• graph::spanning_tree::maximum_spanning_forest
• graph::spanning_tree::minimum_spanning_forest
• methods::cis_target::calculate_aucs
• methods::cis_target::calculate_nes
• methods::cis_target::parse_rcc_type
• methods::cis_target::process_gene_set
• methods::coremo::cluster_stability
• methods::coremo::intersection_size_sorted
• methods::coremo::split_cor_mat_by_sign
• methods::dgrdl::grsc_admm
• methods::diffcor::calculate_diff_correlation
• methods::graph_diffusions::parse_tied_sum
• methods::graph_diffusions::tied_diffusion_parallel
• methods::ica::fast_ica_exp
• methods::ica::fast_ica_logcosh
• methods::ica::parse_ica_type
• methods::ica::prepare_whitening
• methods::ica::stabilised_ica_cv
• methods::ica::stabilised_ica_iters
• methods::lda::lda_fit
• methods::lda::lda_k_sweep
• methods::lda::metrics::arun_2010
• methods::lda::metrics::cao_juan_2009
• methods::lda::metrics::lda_metrics
• methods::lda::metrics::mimno_2011_coherence
• methods::lda::metrics::select_best_k
• methods::lda::parse_lda_learning
• methods::lda::vb::lda_bound
• methods::multi_cca::multi_cca
• methods::multi_cca::multi_cca_permute
• methods::nmf_bulk::nmf_consensus_run
• methods::nmf_bulk::nmf_k_sweep_run
• methods::nmf_bulk::nmf_multiple_run
• methods::nmf_bulk::nmf_single_run
• methods::nmf_hals::compute_objective
• methods::nmf_hals::consensus::consensus_from_restarts
• methods::nmf_hals::consensus::median
• methods::nmf_hals::consensus::nmf_consensus
• methods::nmf_hals::consensus::nmf_k_sweep
• methods::nmf_hals::consensus::parse_consensus_target
• methods::nmf_hals::gram_h_ht
• methods::nmf_hals::gram_wt_w
• methods::nmf_hals::hals_sweep_cols
• methods::nmf_hals::hals_sweep_rows
• methods::nmf_hals::nmf_hals
• methods::nmf_hals::nmf_preprocessing::ensure_csc
• methods::nmf_hals::nmf_preprocessing::nmf_process_dense
• methods::nmf_hals::nmf_preprocessing::nmf_process_sparse
• methods::nmf_hals::nmf_preprocessing::parse_nmf_processing
• methods::nmf_hals::nndsvd_from_svd
• methods::nmf_hals::normalise_w_cols
• methods::nmf_hals::parse_nmf_init
• methods::nmf_hals::random_init
• methods::nmf_hals::refit::nmf_refit_h
• methods::nmf_hals::refit::nmf_refit_w
• methods::nmf_hals::stabilised_nmf
• methods::rbh::calculate_rbh_cor
• methods::rbh::calculate_rbh_set
• methods::snf::make_affinity_categorical
• methods::snf::make_affinity_continuous
• methods::snf::make_affinity_mixed
• methods::snf::snf
• methods::snf::snf_gower_dist
• ontology::go_elim::finalise_go_res
• ontology::go_elim::process_ontology_level
• ontology::go_elim::process_ontology_level_fgsea_simple
• ontology::similarity::calculate_onto_sim
• ontology::similarity::filter_sims_critval
• prelude::array_max
• prelude::array_max_min
• prelude::array_min
• prelude::colbind_matrices
• prelude::column_slices
• prelude::cumsum
• prelude::faer_diagonal_from_vec
• prelude::faer_mat_to_upper_triangle
• prelude::flat_row_major_to_mat
• prelude::flatten_vector
• prelude::mat_rm_row
• prelude::mat_to_flat_row_major
• prelude::min_max_scale
• prelude::nested_vector_to_faer_mat
• prelude::parse_compressed_sparse_format
• prelude::parse_verbosity_level
• prelude::rank_normalise
• prelude::report_decile_progress
• prelude::robust_scale
• prelude::rowbind_matrices
• prelude::split_vector_randomly
• prelude::thread_chunks
• prelude::unique
• prelude::upper_triangle_indices
• prelude::upper_triangle_to_sym_faer
• prelude::zscore_normalise

Type Aliases

• enrichment::gsea::MultiLevelErrRes
• enrichment::mitch::MitchPathways
• ontology::go_elim::AncestorMap
• ontology::go_elim::GeneMap
• ontology::go_elim::LevelMap
• ontology::similarity::SValueCache

Constants

• graph::knn_graph::SNN_PRUNE_DEFAULT
• methods::lda::DEFAULT_MIN_TOPICS_COH
• methods::lda::DEFAULT_TOP_TOPICS_COH
• prelude::MAD_SCALE