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 |
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