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| 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 |
| artmsEvidenceToSaintExpress | MaxQuant evidence file to SAINTexpress format |
| artmsEvidenceToSAINTq | MaxQuant evidence file to SAINTq 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) |
| 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 'Proteins' column of the evidence file to site-specific 'Uniprot_PTM' 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 |
| artmsReplicatePlots | Create the replicate plots based on the pairings from the replicate plot file |
| 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_evidence | Evidence file example |
| artms_data_ph_keys | Keys File Example |
| artms_data_ph_msstats_results | MSstats results file example |
| artms_data_randomDF | Random data set |