MarioniLab/scran
Methods for Single-Cell RNA-Seq Data Analysis

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295
Source code
86
Man pages
47
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MarioniLab/scran: Methods for Single-Cell RNA-Seq Data Analysis
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API

API for MarioniLab/scran
Methods for Single-Cell RNA-Seq Data Analysis

Global functions
.add_log_values Source code
.add_row_data Source code
.average_effect_across_blocks Source code
.blocked_binom Source code
.blocked_wilcox Source code
.buildKNNGraph Source code
.buildSNNGraph Source code
.calculate_rho Source code
.centered_SVD Source code
.check_element_names Source code
.choose_effect_size Source code
.choose_leftright_pvalues Source code
.collate_into_DataFrame Source code
.combine_blocked_statistics Source code
.combine_markers_internal Source code
.compute_all_effect_sizes Source code
.compute_auc Source code
.compute_binom_effect Source code
.compute_lfc_detected Source code
.compute_mean_var Source code
.compute_offsets_by_lfc Source code
.compute_pairwise_cohen_d Source code
.compute_tricube_average Source code
.compute_var_stats_with_spikes Source code
.correct_logged_expectation Source code
.correlate_pairs Source code
.correlator_base Source code
.create_full_stats Source code
.create_rank_matrix Source code
.cross_reference_to_desired Source code
.cyclone Source code
.cyclone_scores Source code
.decompose_cv2 Source code
.decompose_log_exprs Source code
.expand_pairings Source code
.expand_pairings_core Source code
.extract_columns Source code
.extractor Source code
.findMarkers Source code
.find_other_fields Source code
.fit_lm_internal 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
.group_block_combinations Source code
.group_by_used_combinations Source code
.identify_effects_to_average Source code
.inverse_density_weights Source code
.logBH Man page Source code
.mapply_bind 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
.pca_to_output Source code
.process_corr_pairings Source code
.process_subset_for_pca Source code
.pseudo_bulk_dge Source code
.pseudo_bulk_edgeR Source code
.pseudo_bulk_master Source code
.pseudo_bulk_specific Source code
.pseudo_bulk_voom Source code
.quick_cluster Source code
.quick_sub_cluster Source code
.reindex_comparisons_for_combinations Source code
.reorder_pairwise_output Source code
.run_t_test Source code
.scoreMarkers 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
.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
.uniquify_DataFrame 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 Source code
choose_middle_effect_size Source code
clusterCells Man page Source code
clusterKNNGraph Man page Source code
clusterModularity Man page Source code
clusterPurity Man page Source code
clusterSNNGraph Man page Source code
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_rho Source code
computeMinRank 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
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 Source code
doubletCluster Man page Source code
doubletRecovery Man page Source code
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
fixedPCA 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
orderClusterMST Man page Source code
overlapExprs Man page Source code
overlap_exprs Source code
overlap_exprs_paired 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
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
rhoToPValue Man page Source code
sandbag Man page
sandbag,ANY-method Man page
sandbag,SummarizedExperiment-method Man page
scaledColRanks Man page Source code
scoreMarkers Man page
scoreMarkers,ANY-method Man page
scoreMarkers,SingleCellExperiment-method Man page
scoreMarkers,SummarizedExperiment-method Man page
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 Source code
testVar Man page Source code
trendVar Man page Source code
MarioniLab/scran documentation built on Sept. 7, 2024, 6:25 a.m.

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