artmsAnalysisQuantifications
                        Analysis of the Relative Quantifications
artmsAnnotateSpecie     Adding a column with the species name
artmsAnnotationUniprot
                        Annotate table with Gene Symbol and Name based
                        on Uniprot ID(s)
artmsAvgIntensityRT     Summarize average intensity and retention time
                        per protein
artmsChangeColumnName   Change a specific column name in a given
                        data.frame
artmsConvertMetabolomics
                        Convert Markview Metabolomics file (alignment
                        table) into a artMS compatible format
artmsDataPlots          Individual Normalized abundance dot plots for
                        every protein
artmsEnrichLog2fc       Enrichment of changes in protein abundance or
                        PTMs
artmsEnrichProfiler     Enrichment analysis using GprofileR
artmsEvidenceToSAINTq   MaxQuant evidence file to SAINTq format
artmsEvidenceToSaintExpress
                        MaxQuant evidence file to SAINTexpress format
artmsFilterEvidenceContaminants
                        Remove contaminants and empty proteins from the
                        MaxQuant evidence file
artmsGeneratePhSiteExtended
                        Generate ph-site specific detailed file
artmsIsEvidenceNewVersion
                        Check if a given evidencee file was generated
                        by a new version of MaxQuant (v>1)
artmsIsSpeciesSupported
                        Check if a species is supported and available
artmsLeaveOnlyUniprotEntryID
                        Leave only the Entry ID from a typical full
                        Uniprot IDs in a given column
artmsMapUniprot2Entrez
                        Map GENE SYMBOL, NAME, AND ENTREZID to a vector
                        of Uniprot IDS
artmsMergeEvidenceAndKeys
                        Merge evidence.txt (or summary.txt) with
                        keys.txt files
artmsMsstatsSummary     Summarize the MSStats results and data
                        quantification
artmsPhosfateOutput     Generate Phosfate Input file
artmsPhotonOutput       Generate PHOTON Input file
artmsPlotHeatmapQuant   Outputs a heatmap of the MSStats results
                        created using the log2fold changes
artmsProtein2SiteConversion
                        Converts the Protein ID column of the evidence
                        file selected by the user to mod-site-specific
                        notation: 'ProteinID' to 'ProteinID_AAnumber'
                        notation
artmsQualityControlEvidenceBasic
                        Quality Control analysis of the MaxQuant
                        evidence file
artmsQualityControlEvidenceExtended
                        Extended Quality Control of the MaxQuant
                        evidence.txt file
artmsQualityControlMetabolomics
                        Quality Control analysis of the evidence-like
                        metabolomics dataset
artmsQualityControlSummaryExtended
                        Quality Control of the MaxQuant summary.txt
                        file
artmsQuantification     Relative quantification using MSstats
artmsResultsWide        Reshape the MSstats results file from long to
                        wide format
artmsSILACtoLong        Convert the SILAC evidence file to MSstats
                        format
artmsSpectralCounts     Outputs the spectral counts from the MaxQuant
                        evidence file.
artmsVolcanoPlot        Volcano plot (log2fc / pvalues)
artmsWriteConfigYamlFile
                        Write out a template file of the artMS
                        configuration file (yaml)
artms_config            artMS configuration template
artms_data_corum_mito_database
                        CORUM Protein Complexes database use for
                        complex enrichment analysis
artms_data_pathogen_LPN
                        LPN PATHOGEN: Legionella pneumophila subsp.
                        pneumophila (strain Philadelphia 1 / ATCC 33152
                        / DSM 7513) UNIPROT IDS
artms_data_pathogen_TB
                        TB PATHOGEN: Mycobacterium tuberculosis (strain
                        ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDS
artms_data_ph_config    artMS configuration for the available PH
                        dataset
artms_data_ph_contrast
                        Contrast example for the PH dataset
artms_data_ph_evidence
                        Evidence file example
artms_data_ph_keys      Keys File Example
artms_data_ph_msstats_modelqc
                        MSstats modelQC example
artms_data_ph_msstats_results
                        MSstats results example
artms_data_randomDF     Random data set
