CharacterNumbers        Transformation of a vector of integers into a
                        vector of class "character".
ColnamesToFactors       Extraction of factors information and suitable
                        column names creation from the column names of
                        a dataset.
DATAnormalization       Normalization of raw counts (Main Function).
DATAplotBoxplotSamples
                        Visualization of the distribution of all gene
                        expressions using a boxplot for each sample.
DATAplotExpression1Gene
                        Plot expression of one gene.
DATAplotExpressionGenes
                        Plot expression of a subset of genes.
DATAprepSE              Data preparation for exploratory and
                        statistical analysis (Main Function)
DEanalysisGlobal        Realization of the DE analysis (Main Function).
DEanalysisGroup         DE Analysis when samples belong to different
                        biological conditions.
DEanalysisSubData       Sub data of a data.frame
DEanalysisTime          DE analysis when samples belong to different
                        time points only.
DEanalysisTimeAndGroup
                        DE analysis when samples belong to different
                        biological condition and time points.
DEplotAlluvial          Alluvial graphs of differentially expressed
                        (DE) genes
DEplotBarplot           Barplot of DE genes from a contingency table.
DEplotBarplotFacetGrid
                        Faceted barplot of specific DE genes
DEplotBarplotTime       Barplot of DE genes per time
DEplotHeatmaps          Heatmaps of DE genes
DEplotVennBarplotGroup
                        Venn barplot of DE genes across pairs of
                        biological conditions.
DEplotVennBarplotTime   Venn barplot of DE genes across time.
DEplotVolcanoMA         Volcano and MA graphs
DEresultGroup           Intermediate analysis when samples belong to
                        different biological conditions
DEresultGroupPerTime    Intermediate analysis when samples belong to
                        different biological conditions and different
                        time points.
GSEAQuickAnalysis       GSEA analysis with gprofiler2
GSEApreprocessing       GSEA preprocessing for official software and
                        online tools.
HCPCanalysis            Hierarchical clustering analysis with HCPC
                        (Main function)
MFUZZanalysis           Clustering of temporal patterns (Main
                        function).
MFUZZclustersNumber     Automatic choice of the number of clusters to
                        use for the Mfuzz analysis
PCAanalysis             Automatic PCA analysis (Main function)
PCAgraphics             Multiple 2D and 3D PCA graphs.
PCApreprocessing        Reshaped dataset for factorial analysis.
PCArealization          PCA realization
RawCountsSimulation     RNA-seq raw counts data simulation
RawCounts_Antoszewski2022_MOUSEsub500
                        Mouse raw counts data
RawCounts_Leong2014_FISSIONsub500wt
                        Yeast times series raw counts data after
                        stimulation with and without silencing
RawCounts_Schleiss2021_CLLsub500
                        Human CCL times series raw counts data after
                        stimulation with and without silencing
RawCounts_Weger2021_MOUSEsub500
                        Mouse count data with four biological
                        conditions, six time measurements and 500
                        genes.
Results_DEanalysis_sub500
                        DE results of three dataset
Transcript_HomoSapiens_Database
                        Homo sapiens transcript database
