Man pages for vari-bbc/bbcRNA
Bulk RNA-seq workflow for VAI BBC
| aln_metrics | Getter for aln_metrics slot |
| aln_metrics-set | Setter for aln_metrics slot |
| batch_correct_norm_cts | Batch correct normalized counts |
| BbcEdgeR | Constructor for BbcEdgeR |
| BbcEdgeR-class | BbcEdgeR, a class for storing an edgeR analysis |
| bbcRNA | bbcRNA: Bulk RNA-seq workflow for VAI BBC.. |
| BbcSE | Constructor for BbcSE |
| BbcSE-class | BbcSE, an extension of SummarizedExperiment for VAI BBC... |
| cbind-BbcSE-method | Column combining method for BbcSE |
| de_results | Getter for de_results slot from BbcEdgeR object |
| de_results-set | Setter for de_results slot in a BbcEdgeR object |
| deseq2 | Getter for deseq2 slot |
| dgelist | Getter for dgelist slot from BbcEdgeR object |
| dgelist-set | Setter for dgelist slot in a BbcEdgeR object |
| edger | Getter for edger slot |
| edger-set | Setter for edger slot |
| ens2entrez | Convert Ensembl IDs to Entrez IDs for gene enrichment... |
| ens2sym | Convert Ensembl IDs to gene symbols. |
| findDEGs | Identify DE genes. |
| find_missing_in_gseaResult | Compare genes in clusterProfiler gseaResult to genes in a... |
| get_de_table | Get a table of DE results |
| lists_to_edger_contrasts | Function to convert to edgeR-style contrasts |
| makeDGEList | Make a DGEList object. |
| normalize_counts | Calculate normalized counts. |
| norm_cts | Getter for norm_cts slot from BbcEdgeR object |
| norm_cts-set | Setter for norm_cts slot in a BbcEdgeR object |
| plot_aln_metrics | Plot alignment metrics |
| plot_heatmap | Plot heatmap |
| plot_PCA | PCA, screeplot and PERMANOVA test |
| plot_pval_distrib | Plot P-values |
| plot_volcano | Volcano plot |
| prep_clusterprofiler_genelist | Prep clusterProfiler geneList |
| rbind-BbcSE-method | Row combining method for BbcSE |
| read_col_meta | Read column meta data |
| read_star_aln_metrics | Import STAR Log.final.out files for analyzing mapping rates. |
| run_gsea | Run GSEA |
| run_hypergeometric | Run hypergeometric test |
| searchBM | Search biomart datasets with keyword |
| shorten_desc | Shorten Description names from ClusterProfiler results. |
| show-BbcSE-method | show method for BbcSE |
| star_to_mat | Convert STAR read counts to count matrix. |
| sub-BbcSE-ANY-ANY-ANY-method | Subsetting method for BbcSE |
| subset-BbcSE-ANY-ANY-BbcSE-method | Assigning subsets method for BbcSE |
