Man pages for spell098/rnaseq_app
| addColorsMatrix | Annotation of a matrix with colors for contrast values |
| addColorsMatrixResults | Annotation of a matrix with colors from standardized values |
| affy2ensembl | Convert affyId to ensemblID |
| annotate_ensembl | Takes an ensembl_gene_id |
| annotation_geo | Get the annotations used in a NCBI GEO dataset |
| boxplot_element | Generate boxplots of every groups for a selected gene. Also... |
| clusteringSummary | Get the annotations used in a NCBI GEO dataset |
| color_groups | Add color to each sample. Samples with the same color belong... |
| colorNumericValues | Transform intensity values in a gradient of color from green... |
| comparisonsPheno | Transform intensity values in a gradient of color from green... |
| conditionsChoice | Transform intensity values in a gradient of color from green... |
| design_contrasts | Create a design matrix for linear models analysis |
| export2cytoscape | Export results in cytoscape format |
| exprToBind | Binds an expression matrix with colors corresponding to the... |
| fuzzy_clustering | Find the groups using fuzzy clustering ##FIND AUTOMATICALLY... |
| geneOntology | List of informations on Gene Ontology of selected genes |
| get_comparisons | Take all the name and export all possible comparisons |
| get_names | Get names of each sample and group names |
| lm2Contrast | Linear Model analysis with limma |
| MAPlot | Generates a MAPlot with ggplot |
| meanMatrix | Mean matrix |
| modules_summary | Returns the summary for a module |
| namesSelectedComparisons | Create a vector of the group membership for each sample |
| network.graphite | Create a graphNEL graph with directed edges from the results... |
| numberNames | Add increasing number at the end of all strings. Duplicated... |
| order_list | Order the element of a list by size in decreasing order |
| PCA | Displays a Princpial component analysis graph. USE GGPLOT!! |
| plotCorrectAttribution | Plot the groups correctly attributed |
| plotCorrectSubsample | Plot the subsamples correctly attributed |
| possibleComparisons | Possible Comparisons |
| RDA_factors | RDA plots Creates a biplot |
| reactions | Top reactions |
| resultsByOntology | Results by ontology Return the rows from the results topTable |
| results_summary | Summary of the results Create a data.frame that displays... |
| results_topTable | Calculate results |
| selectTopReaction | Select a reaction from a top reactions table |
| signifRows | Select in an expression matrix only the rows with significant... |
| transcript_count | Counts the number of significant transcripts of the same gene |
| volcanoPlot | Generates a volcanoplot with ggplot |
| wes | Simple function to get color palettes from the wesanderson... |
| WGCNA_modules | Find to which genes belong to the same modules |
