API for SpitzerLab/statisticalScaffold
SCAFFoLD
| Global functions | |
|---|---|
| SAM | Source code |
| adaptive_expand | Source code |
| add_attractors_labels | Source code |
| add_inter_clusters_connections | Source code |
| add_missing_columns | Source code |
| add_vertices_to_attractors_graph | Source code |
| analyze_cluster_correlation | Source code |
| analyze_cluster_expression | Source code |
| analyze_cluster_frequencies | Source code |
| append_corr_signif | Source code |
| append_expr_signif | Source code |
| append_freq_signif | Source code |
| buildBooleanMatrix | Source code |
| build_graph | Source code |
| calculate_FoldChange | Source code |
| check.format | Source code |
| check_names | Source code |
| cleanPlotMarkers | Source code |
| cluster_data | Source code |
| cluster_fcs_files_groups | Source code |
| cluster_fcs_files_in_dir | Source code |
| complete.forceatlas2 | Source code |
| compute.block.perms | Source code |
| convert_fcs | Source code |
| cosine_similarity_from_matrix | Source code |
| cosine_similarity_matrix | Source code |
| cox.func | Source code |
| cox.seq.func | Source code |
| density_scatterplot | Source code |
| detec.horiz | Source code |
| detec.slab | Source code |
| distance_from_attractor_hard_filter | Source code |
| downsample_by | Source code |
| est.s0 | Source code |
| export_clusters | Source code |
| export_clusters_all_files | Source code |
| extractColnames | Source code |
| filter_similarity_matrix | Source code |
| filter_similarity_matrix_by_rank | Source code |
| filter_small_populations | Source code |
| foldchange.paired | Source code |
| foldchange.seq.twoclass.paired | Source code |
| foldchange.seq.twoclass.unpaired | Source code |
| foldchange.twoclass | Source code |
| generate.dels | Source code |
| getFrequencies | Source code |
| getSampleIDs | Source code |
| getSignifMatrix | Source code |
| getTotalCellNumbers | Source code |
| get_attractors_from_graph_clustering | Source code |
| get_celltype_medians | Source code |
| get_cluster_label | Source code |
| get_color_for_marker | Source code |
| get_dataset_statistics | Source code |
| get_distances_from_attractors | Source code |
| get_fcs_col_names | Source code |
| get_graph | Source code |
| get_graph_centering_transform | Source code |
| get_graph_table | Source code |
| get_highest_scoring_edges | Source code |
| get_num_clusters | Source code |
| get_number_of_cells_per_landmark | Source code |
| get_numeric_vertex_attributes | Source code |
| get_rdata_col_names | Source code |
| get_stats_by_sample | Source code |
| get_summary_table | Source code |
| get_vertex_size | Source code |
| get_vertex_table | Source code |
| getperms | Source code |
| insert.value | Source code |
| integer.base.b | Source code |
| layout.forceatlas2 | Source code |
| layout_forceatlas2Cpp | Source code |
| load_attractors_from_gated_data | Source code |
| load_existing_layout | Source code |
| localfdr | Source code |
| mark_nearest_neighbour | Source code |
| multiclass.func | Source code |
| multiclass.seq.func | Source code |
| my_load | Source code Source code |
| my_save | Source code |
| mysvd | Source code |
| names_map_factory | Source code |
| onesample.ttest.func | Source code |
| paired.ttest.func | Source code |
| parse.block.labels.for.2classes | Source code |
| parse.time.labels.and.summarize.data | Source code |
| patterndiscovery.func | Source code |
| permute | Source code |
| permute.rows | Source code |
| plot.SAMoutput | Source code |
| plot_cluster | Source code |
| predictlocalfdr | Source code |
| print.SAMoutput | Source code |
| print_Feature_Template | Source code |
| process_data | Source code |
| process_file | Source code |
| process_files | Source code |
| process_files_groups | Source code |
| process_files_together | Source code |
| quantitative.func | Source code |
| quantitative.seq.func | Source code |
| qvalue.func | Source code |
| rankcol | Source code |
| remove_correlation_columns | Source code |
| remove_exprsignif_columns | Source code |
| remove_freqsignif_columns | Source code |
| resample | Source code |
| rescale_size | Source code |
| runSAM | Source code |
| run_SAM_analysis | Source code |
| run_analysis_existing | Source code |
| run_analysis_gated | Source code |
| run_analysis_unsupervised | Source code |
| sample.perms | Source code |
| samr | Source code |
| samr.assess.samplesize | Source code |
| samr.assess.samplesize.plot | Source code |
| samr.compute.delta.table | Source code |
| samr.compute.delta.table.array | Source code |
| samr.compute.delta.table.seq | Source code |
| samr.compute.siggenes.table | Source code |
| samr.estimate.depth | Source code |
| samr.missrate | Source code |
| samr.norm.data | Source code |
| samr.plot | Source code |
| samr.pvalues.from.perms | Source code |
| samr.seq.detec.slabs | Source code |
| samr.seq.null.err | Source code |
| samr.tail.strength | Source code |
| scaffold | Man page |
| scaffold-package | Man page |
| scaffold.run | Source code |
| set_visual_attributes | Source code |
| sumlengths | Source code |
| timearea.func | Source code |
| ttest.func | Source code |
| varr | Source code |
| wilcoxon.func | Source code |
| wilcoxon.paired.seq.func | Source code |
| wilcoxon.unpaired.seq.func | Source code |
