Man pages for crickbabs/RNASeq-DESeq
DESeq2 Wrapper For Pre-Specified Analyses
| add_dim_reduct | Store dimension-reduction results in DESeq2 object |
| bookdown_label | Multiple GT tables per chunk |
| build_dds_list | Generate subsets of DESeq2 object |
| captioner | Caption hyperlinking |
| check_model | Check model |
| d3_iMetric | Interactive metric plot |
| d3_iMetric-shiny | Shiny bindings for d3_iMetric |
| d3_iScatter | Interactive PCA plot |
| d3_iScatter-shiny | Shiny bindings for d3_iScatter |
| df2colorspace | Heatmap colour-scheme generator |
| differential_heatmap | Heatmaps of differential genes |
| differential_MA | Generate MA Plots |
| emcontrasts | Expand multiple comparisons into their contrasts |
| enrichment | Geneset enrichment analysis |
| export_biologic | Export Biologic files |
| extract_assay | Return an assay from a result-list |
| extract_colData | Return PCA-projected data from a result-list |
| extract_pca_x | Return PCA-projected data from a result-list |
| extract_results | Return all results contained in a result list |
| fitLRT | Fit LRT |
| fit_models | Fit the DESeq2 models |
| get_result | Generate the results for a model and comparison |
| get_started | Initiate a DESdemonA project |
| klabel | deprecated |
| load_specs | Adjust a confounded batch effect |
| map_des | Wrap datasets from DESdemonA |
| mult_comp | Mark a formula as a multiple comparison |
| over_representation | Geneset over-representation analysis |
| ParamList | R6 class representing the set of parameters used in an... |
| qc_heatmap | Data Visualisation |
| rbind_summary | rbind nested lists of data-frames |
| rebase | Rebase a factor's level |
| recode_within | Recode nested factors |
| results_apply | Apply a function to a results list |
| run_report | Run DESdemonA Report on existing counts object |
| subsample | subsample |
| summarise_results | Tabulate the size of the differential lists |
| table1 | Table One |
| tab_link_caption | Link GT tables to a csv file |
| write_all_results | Store results as text files |
| write_assay | Text file of assay data |
| write_results | XLSX report of results |
