Man pages for spell098/rnaseq_app

addColorsMatrixAnnotation of a matrix with colors for contrast values
addColorsMatrixResultsAnnotation of a matrix with colors from standardized values
affy2ensemblConvert affyId to ensemblID
annotate_ensemblTakes an ensembl_gene_id
annotation_geoGet the annotations used in a NCBI GEO dataset
boxplot_elementGenerate boxplots of every groups for a selected gene. Also...
clusteringSummaryGet the annotations used in a NCBI GEO dataset
color_groupsAdd color to each sample. Samples with the same color belong...
colorNumericValuesTransform intensity values in a gradient of color from green...
comparisonsPhenoTransform intensity values in a gradient of color from green...
conditionsChoiceTransform intensity values in a gradient of color from green...
design_contrastsCreate a design matrix for linear models analysis
export2cytoscapeExport results in cytoscape format
exprToBindBinds an expression matrix with colors corresponding to the...
fuzzy_clusteringFind the groups using fuzzy clustering ##FIND AUTOMATICALLY...
geneOntologyList of informations on Gene Ontology of selected genes
get_comparisonsTake all the name and export all possible comparisons
get_namesGet names of each sample and group names
lm2ContrastLinear Model analysis with limma
MAPlotGenerates a MAPlot with ggplot
meanMatrixMean matrix
modules_summaryReturns the summary for a module
namesSelectedComparisonsCreate a vector of the group membership for each sample
network.graphiteCreate a graphNEL graph with directed edges from the results...
numberNamesAdd increasing number at the end of all strings. Duplicated...
order_listOrder the element of a list by size in decreasing order
PCADisplays a Princpial component analysis graph. USE GGPLOT!!
plotCorrectAttributionPlot the groups correctly attributed
plotCorrectSubsamplePlot the subsamples correctly attributed
possibleComparisonsPossible Comparisons
RDA_factorsRDA plots Creates a biplot
reactionsTop reactions
resultsByOntologyResults by ontology Return the rows from the results topTable
results_summarySummary of the results Create a data.frame that displays...
results_topTableCalculate results
selectTopReactionSelect a reaction from a top reactions table
signifRowsSelect in an expression matrix only the rows with significant...
transcript_countCounts the number of significant transcripts of the same gene
volcanoPlotGenerates a volcanoplot with ggplot
wesSimple function to get color palettes from the wesanderson...
WGCNA_modulesFind to which genes belong to the same modules
spell098/rnaseq_app documentation built on May 26, 2017, 3:25 p.m.