Man pages for johannesnicolaus/ASURAT_source
Assisting Interpretable Classifications in Single-cell Transcriptomics
| asurat_add_qcmetrics | Compute QC metrics for each sample. |
| asurat_quick_genefilter | Remove rarely expressed genes. |
| auto_find_marker_gene | Title |
| auto_find_marker_sign | Title |
| cerv_asurat | Single-cell RNA-seq data of human cervix cancer cells |
| classify_samples_hclustCutree_sign | Title |
| classify_samples_merlot_sign | Title |
| classify_samples_pam_sign | Perform sample classification using Partitioning Around... |
| classify_samples_seuratFindClusters_sign | Title |
| collect_CO | Title |
| collect_DO | Import Disease Ontology database |
| collect_GO | Import Gene Ontology database |
| collect_KEGG | Import KEGG database |
| collect_Reactome | Import Reactome database |
| compute_IC_CO | Title |
| compute_IC_DO | Calculates information content (IC) from Disease Ontology... |
| compute_IC_GO | Calculates information content (IC) from Gene Ontology data |
| compute_nswaps | Title |
| compute_SemSim_sign | Computes pairwise semantic similarities between the... |
| concatenate_obj_sign | Title |
| do_CalculateElasticTree_dmap | Title |
| do_CalculatePseudotimes_dmap | Title |
| do_CalculateScaffoldTree_dmap | Title |
| do_cellTypeToGenes | Title |
| do_DiffusionMap_sign | Title |
| do_enrichGO_seurat | Title |
| do_groupGO | ***Please clarify*** |
| do_keggGet | ***Please clarify*** |
| do_pca_sign | Title |
| do_quickQC | Perform quick QC |
| do_quickQC_sign | Perform quick QC for ? |
| do_SignSpaceEmbedding_dmap | Title |
| do_simplifyGO_seurat | Title |
| do_tsne_sign | Title |
| do_umap_sign | Title |
| find_descendants | Title |
| find_marker_gene | Title |
| find_marker_sign | Title |
| format_CO | Title |
| format_DO | Formats the result of imported DO database |
| format_GO | Title |
| format_KEGG | Format KEGG database to be ASURAT-friendly |
| format_Reactome | Format imported downloaded Reactome database to... |
| get_CO | Wrapper function to get Cell Ontology database |
| get_db | Title |
| get_DO | Wrapper function to import Disease Ontology database |
| get_GO | Wrapper function to import Gene Ontology database |
| get_KEGG | Wrapper function to import KEGG database |
| get_Reactome | Wrapper function to import Reactome database |
| make_asurat_obj | Make an ASURAT object. |
| make_signxsample_matrix | Make sign by sample matrix |
| make_treeTable_CO | Title |
| manual_curation_sign | Removes biological terms by specifying IDs or keywords |
| manual_selection_sign | Title |
| pbmc_asurat | Single-cell RNA-seq data of peripheral blood mononuclear... |
| plot_bargraph_seurat | Title |
| plot_GOemapplot_seurat | Title |
| plot_pcaEigen_seurat | Title |
| plot_tsne_nReads_seurat | Title |
| plot_tsne_seurat | Title |
| plot_tsne_signExpression_seurat | Title |
| plot_umap_seurat | Title |
| plot_umap_signExpression_seurat | Title |
| plot_variableFeatures_seurat | Title |
| process_001_seurat | Performs data processing using Seurat |
| process_002_seurat | Title |
| reduce_sign | Reduce biological terms |
| select_sign | Select signs by user-defined criteria |
| separate_variables_sign | Classify genes annotated with each biological description... |
| trim_samples | Filter samples by previously calculated single-cell metrics |
| trim_variables | Remove low quality genes |
