scran
Methods for Single-Cell RNA-Seq Data Analysis

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319
Source code
95
Man pages
55
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API for scran
Methods for Single-Cell RNA-Seq Data Analysis

Global functions
.add_log_values Source code
.add_row_data Source code
.blocked_binom Source code
.blocked_wilcox Source code
.buildKNNGraph Source code
.buildSNNGraph Source code
.calculate_rho Source code
.calculate_sum_factors Source code
.centered_SVD Source code
.check_element_names Source code
.check_null_dist Source code
.choose_effect_size Source code
.choose_gene_names Source code
.choose_leftright_pvalues Source code
.clusterKNNGraph Source code
.clusterSNNGraph Source code
.clusterXNNGraph Source code
.cluster_purity Source code
.combine_blocked_statistics Source code
.combine_markers_internal Source code
.compute_binom_effect Source code
.compute_mean_var Source code
.compute_offsets_by_lfc Source code
.compute_tricube_average Source code
.compute_var_stats_with_spikes Source code
.construct_pair_indices Source code
.correct_logged_expectation Source code
.correlate_pairs Source code
.correlator_base Source code
.create_full_stats Source code
.create_linear_system Source code
.create_rank_matrix Source code
.cyclone Source code
.cyclone_scores Source code
.decompose_cv2 Source code
.decompose_log_exprs Source code
.doublet_cells Source code
.doublet_cluster Source code
.doublet_recovery Source code
.estimate_edge_confidence Source code
.extract_columns Source code
.extractor Source code
.findMarkers Source code
.find_other_fields Source code
.fit_lm_internal Source code
.forge_spline_basis_design Source code
.generateSphere Source code
.generate_lfc_binom Source code
.generate_lfc_wilcox Source code
.generate_nolfc_binom Source code
.generate_nolfc_wilcox Source code
.generate_poisson_values Source code
.get_denoised_pcs Source code
.get_nls_starts Source code
.get_scaled_ranks Source code
.get_sigma Source code
.get_t_test_stats Source code
.guess_min_mean Source code
.inverse_density_weights Source code
.is_sig_limited Source code
.keep_rank_in_range Source code
.limit_cluster_size Source code
.logBH Man page Source code
.map2edges Source code
.merge_closest_graph Source code
.model_gene_cv2 Source code
.model_gene_cv2_with_spikes Source code
.model_gene_var Source code
.model_gene_var_by_poisson Source code
.model_gene_var_with_spikes Source code
.niters_by_nworkers Source code
.pairwiseBinom Source code
.pairwiseTTests Source code
.pairwiseWilcox Source code
.pairwise_blocked_internal Source code
.pairwise_blocked_template Source code
.per_cluster_normalize Source code
.pseudo_bulk_dge Source code
.pseudo_bulk_edgeR Source code
.pseudo_bulk_master Source code
.pseudo_bulk_old Source code
.pseudo_bulk_specific Source code
.pseudo_bulk_voom Source code
.quick_cluster Source code
.quick_sub_cluster Source code
.reorder_pairwise_output Source code
.rescale_clusters Source code
.rho_to_pval Source code
.run_t_test Source code
.setup_gene_names Source code
.setup_groups Source code
.setup_knn_data Source code
.setup_nls_args Source code
.setup_pcg_state Source code
.spawn_doublet_pcs Source code
.summarize_coassign Source code
.summary_marker_stats Source code
.svd_to_pca Source code
.svd_to_rot Source code
.test_block_internal Source code
.test_linear_model Source code
.test_linear_model_multiblock Source code
.test_linear_model_simple Source code
.test_multi_pseudotime Source code
.test_pseudotime Source code
.test_solo_pseudotime Source code
.weighted_average_vals Source code
DM Man page Source code
bootstrapCluster Man page Source code
buildKNNGraph Man page
buildKNNGraph,ANY-method Man page
buildKNNGraph,SingleCellExperiment-method Man page
buildSNNGraph Man page
buildSNNGraph,ANY-method Man page
buildSNNGraph,SingleCellExperiment-method Man page
buildSNNGraph,SummarizedExperiment-method Man page
calculateSumFactors Man page
calculateSumFactors,ANY-method Man page
calculateSumFactors,SummarizedExperiment-method Man page
choose_middle_effect_size Source code
cleanSizeFactors Man page Source code
clusterKNNGraph Man page
clusterKNNGraph,ANY-method Man page
clusterKNNGraph,SingleCellExperiment-method Man page
clusterKNNGraph,SummarizedExperiment-method Man page
clusterModularity Man page Source code
clusterPurity Man page
clusterPurity,ANY-method Man page
clusterPurity,SingleCellExperiment-method Man page
clusterPurity,SummarizedExperiment-method Man page
clusterSNNGraph Man page
clusterSNNGraph,ANY-method Man page
clusterSNNGraph,SingleCellExperiment-method Man page
clusterSNNGraph,SummarizedExperiment-method Man page
coassignProb Man page Source code
combineBlocks Man page Source code
combineCV2 Man page Source code
combineMarkers Man page Source code
combinePValues Man page Source code
combineVar Man page Source code
combine_holm_middle Source code
combine_rho Source code
combine_simes Source code
computeSpikeFactors Man page Source code
computeSumFactors Man page Source code
compute_Top_statistic_from_ranks Source code
compute_blocked_stats_lognorm Source code
compute_blocked_stats_none Source code
compute_blocked_stats_norm Source code
compute_residual_stats_lognorm Source code
compute_residual_stats_none Source code
compute_rho_pairs Source code
connectClusterMST Man page Source code
convertTo Man page Source code
correlateGenes Man page Source code
correlateNull Man page Source code
correlatePairs Man page
correlatePairs,ANY-method Man page
correlatePairs,SummarizedExperiment-method Man page
createClusterMST Man page Source code
cyclone Man page
cyclone,ANY-method Man page
cyclone,SummarizedExperiment-method Man page
cyclone_scores Source code
decideTestsPerLabel Man page Source code
decomposeVar Man page Source code
defunct Man page
denoisePCA Man page Source code
denoisePCANumber Man page Source code
doubletCells Man page
doubletCells,ANY-method Man page
doubletCells,SingleCellExperiment-method Man page
doubletCells,SummarizedExperiment-method Man page
doubletCluster Man page
doubletCluster,ANY-method Man page
doubletCluster,SingleCellExperiment-method Man page
doubletCluster,SummarizedExperiment-method Man page
doubletRecovery Man page
doubletRecovery,ANY-method Man page
doubletRecovery,SingleCellExperiment-method Man page
doubletRecovery,SummarizedExperiment-method Man page
find.markers Source code
findMarkers Man page
findMarkers,ANY-method Man page
findMarkers,SingleCellExperiment-method Man page
findMarkers,SummarizedExperiment-method Man page
fitTrendCV2 Man page Source code
fitTrendPoisson Man page Source code
fitTrendVar Man page Source code
getClusteredPCs Man page Source code
getDenoisedPCs Man page
getDenoisedPCs,ANY-method Man page
getDenoisedPCs,SummarizedExperiment-method Man page
getMarkerEffects Man page Source code
getTopHVGs Man page Source code
getTopMarkers Man page Source code
get_null_rho Source code
get_null_rho_design Source code
improvedCV2 Man page Source code
makeTechTrend Man page Source code
modelGeneCV2 Man page
modelGeneCV2,ANY-method Man page
modelGeneCV2,SingleCellExperiment-method Man page
modelGeneCV2,SummarizedExperiment-method Man page
modelGeneCV2WithSpikes Man page
modelGeneCV2WithSpikes,ANY-method Man page
modelGeneCV2WithSpikes,SingleCellExperiment-method Man page
modelGeneCV2WithSpikes,SummarizedExperiment-method Man page
modelGeneVar Man page
modelGeneVar,ANY-method Man page
modelGeneVar,SingleCellExperiment-method Man page
modelGeneVar,SummarizedExperiment-method Man page
modelGeneVarByPoisson Man page
modelGeneVarByPoisson,ANY-method Man page
modelGeneVarByPoisson,SingleCellExperiment-method Man page
modelGeneVarByPoisson,SummarizedExperiment-method Man page
modelGeneVarWithSpikes Man page
modelGeneVarWithSpikes,ANY-method Man page
modelGeneVarWithSpikes,SingleCellExperiment-method Man page
modelGeneVarWithSpikes,SummarizedExperiment-method Man page
multiBlockNorm Man page Source code
multiBlockVar Man page Source code
multiMarkerStats Man page Source code
neighborsToKNNGraph Man page Source code
neighborsToSNNGraph Man page Source code
orderClusterMST Man page Source code
overlapExprs Man page Source code
overlap_exprs Source code
pairwiseBinom Man page
pairwiseBinom,ANY-method Man page
pairwiseBinom,SingleCellExperiment-method Man page
pairwiseBinom,SummarizedExperiment-method Man page
pairwiseTTests Man page
pairwiseTTests,ANY-method Man page
pairwiseTTests,SingleCellExperiment-method Man page
pairwiseTTests,SummarizedExperiment-method Man page
pairwiseWilcox Man page
pairwiseWilcox,ANY-method Man page
pairwiseWilcox,SingleCellExperiment-method Man page
pairwiseWilcox,SummarizedExperiment-method Man page
parallelPCA Man page Source code
pool_size_factors Source code
pseudoBulkDGE Man page
pseudoBulkDGE,ANY-method Man page
pseudoBulkDGE,SummarizedExperiment-method Man page
pseudoBulkSpecific Man page
pseudoBulkSpecific,ANY-method Man page
pseudoBulkSpecific,SummarizedExperiment-method Man page
quickCluster Man page
quickCluster,ANY-method Man page
quickCluster,SummarizedExperiment-method Man page
quickPseudotime Man page Source code
quickSubCluster Man page
quickSubCluster,ANY-method Man page
quickSubCluster,SingleCellExperiment-method Man page
quickSubCluster,SummarizedExperiment-method Man page
sandbag Man page
sandbag,ANY-method Man page
sandbag,SummarizedExperiment-method Man page
scaledColRanks Man page Source code
scran-gene-selection Man page
summarizeTestsPerLabel Man page Source code
summaryMarkerStats Man page
summaryMarkerStats,ANY-method Man page
summaryMarkerStats,SummarizedExperiment-method Man page
technicalCV2 Man page Source code
testLinearModel Man page
testLinearModel,ANY-method Man page
testLinearModel,SummarizedExperiment-method Man page
testPseudotime Man page
testPseudotime,ANY-method Man page
testPseudotime,SummarizedExperiment-method Man page
testVar Man page Source code
trendVar Man page Source code
scran documentation built on April 17, 2021, 6:09 p.m.

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