Tools for the Differential Analysis of Proteins Abundance with R

addOriginOfValue | Sets the OriginOfValues dataframe |

aggregateIter | xxxx |

aggregateIterParallel | xxxx |

aggregateMean | Compute the intensity of proteins as the mean of the... |

aggregateSum | Compute the intensity of proteins with the sum of the... |

aggregateTopn | Compute the intensity of proteins as the sum of the... |

averageIntensities | Average protein/peptide abundances for each condition studied |

barplotEnrichGO_HC | A barplot that shows the result of a GO enrichment, using the... |

barplotGroupGO_HC | A barplot which shows the result of a GO classification,... |

boxPlotD_HC | Builds a boxplot from a dataframe using the library... |

BuildAdjacencyMatrix | Function matrix of appartenance group |

BuildColumnToProteinDataset | creates a column for the protein dataset after agregation by... |

BuildColumnToProteinDataset_par | creates a column for the protein dataset after agregation by... |

buildGraph | Display a CC |

BuildPalette | Builds a complete color palette for the conditions given in... |

checkClusterability | Prepare the data for subsequent clustering |

check.conditions | Check if the design is valid |

check.design | Check if the design is valid |

classic1wayAnova | Function to perform a One-way Anova statistical test on a... |

compareNormalizationD_HC | Builds a plot from a dataframe. Same as compareNormalizationD... |

compute_t_tests | xxxxxx |

corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the... |

CountPep | Compute the number of peptides used to aggregate proteins |

createMSnset | Creates an object of class 'MSnSet' from text file |

CVDistD | Distribution of CV of entities |

CVDistD_HC | Distribution of CV of entities |

dapar_hc_chart | Customised resetZoomButton of highcharts plots |

dapar_hc_ExportMenu | Customised contextual menu of highcharts plots |

deleteLinesFromIndices | Delete the lines in the matrix of intensities and the... |

densityPlotD | Builds a densityplot from a dataframe |

densityPlotD_HC | Builds a densityplot from a dataframe |

diffAnaComputeFDR | Computes the FDR corresponding to the p-values of the... |

diffAnaGetSignificant | Returns a MSnSet object with only proteins significant after... |

diffAnaSave | Returns a 'MSnSet' object with the results of the... |

diffAnaVolcanoplot | Volcanoplot of the differential analysis |

diffAnaVolcanoplot_rCharts | Volcanoplot of the differential analysis |

display.CC.visNet | Display a CC |

enrich_GO | Calculates GO enrichment classes for a given list of... |

finalizeAggregation | Finalizes the aggregation process |

findMECBlock | Finds the LAPALA into a 'MSnSet' object |

formatLimmaResult | xxxx |

formatPHResults | Extract logFC and raw pvalues from multiple post-hoc models... |

fudge2LRT | Heuristic to choose the value of the hyperparameter (fudge... |

Get_AllComparisons | Returns list that contains a list of the statistical tests... |

GetDetailedNbPeptides | Computes the detailed number of peptides for each protein |

GetDetailedNbPeptidesUsed | Computes the detailed number of peptides used for aggregating... |

getIndicesConditions | Gets the conditions indices. |

getIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix... |

getListNbValuesInLines | Returns the possible number of values in lines in the data |

GetNbPeptidesUsed | Computes the number of peptides used for aggregating each... |

getNumberOf | Number of lines with prefix |

getNumberOfEmptyLines | Returns the number of empty lines in the data |

get.pep.prot.cc | Build the list of connex composant of the adjacency matrix |

getPourcentageOfMV | Percentage of missing values |

getProcessingInfo | Returns the contains of the slot processing of an object of... |

getProteinsStats | Computes the number of proteins that are only defined by... |

getQuantile4Imp | Quantile imputation value definition |

getTextForAggregation | Build the text information for the Aggregation process |

getTextForAnaDiff | Build the text information for the Aggregation process |

getTextForFiltering | Build the text information for the filtering process |

getTextForGOAnalysis | Build the text information for the Aggregation process |

getTextForHypothesisTest | Build the text information for the hypothesis test process |

getTextForNewDataset | Build the text information for a new dataset |

getTextForNormalization | Build the text information for the Normalization process |

getTextForpeptideImputation | Build the text information for the peptide Imputation process |

getTextForproteinImputation | Build the text information for the protein Imputation process |

GlobalQuantileAlignment | Normalisation GlobalQuantileAlignement |

GOAnalysisSave | Returns an 'MSnSet' object with the results of the GO... |

GraphPepProt | Function to create a histogram that shows the repartition of... |

group_GO | Calculates the GO profile of a vector of genes/proteins at a... |

hc_logFC_DensityPlot | Density plots of logFC values |

hc_mvTypePlot2 | Distribution of Observed values with respect to intensity... |

heatmapD | This function is a wrapper to 'heatmap.2' that displays... |

heatmap.DAPAR | This function is inspired from the function 'heatmap.2' that... |

histPValue_HC | Plots a histogram ov p-values |

impute.detQuant | Deterministic imputation |

impute.pa2 | Missing values imputation from a 'MSnSet' object |

inner.aggregate.iter | xxxx |

inner.aggregate.topn | xxxx |

inner.mean | xxxx |

inner.sum | xxxx |

is.MV | Similar to the function 'is.na' but focused on the equality... |

is.OfType | Similar to the function 'is.na' but focused on the equality... |

LH0 | xxxxxx |

LH0.lm | xxxxxx |

LH1 | xxxxxx |

LH1.lm | xxxxxx |

limmaCompleteTest | Computes a hierarchical differential analysis |

listSheets | This function returns the list of the sheets names in a Excel... |

LOESS | Normalisation LOESS |

make.contrast | Builds the contrast matrix |

make.design | Builds the design matrix |

make.design.1 | Builds the design matrix for designs of level 1 |

make.design.2 | Builds the design matrix for designs of level 2 |

make.design.3 | Builds the design matrix for designs of level 3 |

MeanCentering | Normalisation MeanCentering |

mvFilter | Filter lines in the matrix of intensities w.r.t. some... |

mvFilterFromIndices | Filter lines in the matrix of intensities w.r.t. some... |

mvFilterGetIndices | Filter lines in the matrix of intensities w.r.t. some... |

mvHisto_HC | Histogram of missing values |

mvImage | Heatmap of missing values |

mvPerLinesHisto_HC | Bar plot of missing values per lines using highcharter |

mvPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per condition |

my_hc_chart | Customised resetZoomButton of highcharts plots |

my_hc_ExportMenu | Customised contextual menu of highcharts plots |

nonzero | Retrieve the indices of non-zero elements in sparse matrices |

normalizeMethods.dapar | List normalization methods with tracking option |

NumericalFiltering | Removes lines in the dataset based on numerical conditions. |

NumericalgetIndicesOfLinesToRemove | Get the indices of the lines to delete, based on a prefix... |

pepa.test | PEptide based Protein differential Abundance test |

plotJitter | Jitter plot of CC |

plotJitter_rCharts | Display a a jitter plot for CC |

plotPCA_Eigen | Plots the eigen values of PCA |

plotPCA_Eigen_hc | Plots the eigen values of PCA with the highcharts library |

plotPCA_Ind | Plots individuals of PCA |

plotPCA_Var | Plots variables of PCA |

postHocTest | Post-hoc tests for classic 1-way ANOVA |

proportionConRev_HC | Barplot of proportion of contaminants and reverse |

QuantileCentering | Normalisation QuantileCentering |

rbindMSnset | Similar to the function 'rbind' but applies on two subsets of... |

readExcel | This function reads a sheet of an Excel file and put the data... |

reIntroduceMEC | Put back LAPALA into a 'MSnSet' object |

removeLines | Removes lines in the dataset based on a prefix string. |

samLRT | xxxxxx |

saveParameters | Saves the parameters of a tool in the pipeline of Prostar |

scatterplotEnrichGO_HC | A dotplot that shows the result of a GO enrichment, using the... |

setMEC | Sets the MEC tag in the OriginOfValues |

splitAdjacencyMat | splits an adjacency matrix into specific and shared |

StringBasedFiltering | Removes lines in the dataset based on a prefix strings... |

StringBasedFiltering2 | Removes lines in the dataset based on a prefix strings. |

SumByColumns | Normalisation SumByColumns |

test.design | Check if xxxxxx |

translatedRandomBeta | Generator of simulated values |

univ_AnnotDbPkg | Returns the totality of ENTREZ ID (gene id) of an OrgDb... |

violinPlotD | Builds a violinplot from a dataframe |

visualizeClusters | Visualize the clusters according to pvalue thresholds |

vsn | Normalisation vsn |

wrapperCalibrationPlot | Performs a calibration plot on an 'MSnSet' object, calling... |

wrapperClassic1wayAnova | Wrapper for One-way Anova statistical test |

wrapper.compareNormalizationD_HC | Builds a plot from a dataframe |

wrapper.corrMatrixD_HC | Displays a correlation matrix of the quantitative data of the... |

wrapper.CVDistD | Distribution of CV of entities |

wrapper.CVDistD_HC | Distribution of CV of entities |

wrapper.dapar.impute.mi | Missing values imputation using the LSimpute algorithm. |

wrapper.hc_mvTypePlot2 | Distribution of observed values with respect to intensity... |

wrapper.heatmapD | This function is a wrapper to 'heatmap.2' that displays... |

wrapper.impute.detQuant | Wrapper of the function 'impute.detQuant' for objects of... |

wrapper.impute.fixedValue | Missing values imputation from a 'MSnSet' object |

wrapper.impute.KNN | KNN missing values imputation from a 'MSnSet' object |

wrapper.impute.mle | Imputation of peptides having no values in a biological... |

wrapper.impute.pa | Imputation of peptides having no values in a biological... |

wrapper.impute.pa2 | Missing values imputation from a 'MSnSet' object |

wrapper.impute.slsa | Imputation of peptides having no values in a biological... |

wrapper.mvHisto_HC | Histogram of missing values from a 'MSnSet' object |

wrapper.mvImage | Heatmap of missing values from a 'MSnSet' object |

wrapper.mvPerLinesHisto_HC | Histogram of missing values per lines from an object using... |

wrapper.mvPerLinesHistoPerCondition_HC | Bar plot of missing values per lines and per conditions from... |

wrapper.normalizeD | Normalisation |

wrapper.pca | Compute the PCA |

wrapperRunClustering | Run a clustering pipeline of protein/peptide abundance... |

writeMSnsetToCSV | Exports a MSnset dataset into a zip archive containing three... |

writeMSnsetToExcel | This function exports a 'MSnSet' object to a Excel file. |

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