Man pages for biodavidjm/artMS
Analytical R tools for Mass Spectrometry
| 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... |
| artmsAvgIntensityRT | Summarize average intensity and retention time per protein |
| artmsChangeColumnName | Change a specific column name in a given data.frame |
| artms_config | artMS configuration template |
| artmsConvertMetabolomics | Convert Markview Metabolomics file (alignment table) into a... |
| artms_data_corum_mito_database | CORUM Protein Complexes database use for complex enrichment... |
| artms_data_pathogen_LPN | LPN PATHOGEN: Legionella pneumophila subsp. pneumophila... |
| artms_data_pathogen_TB | TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 /... |
| 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 |
| artmsDataPlots | Individual Normalized abundance dot plots for every protein |
| artms_data_randomDF | Random data set |
| 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... |
| artmsGeneratePhSiteExtended | Generate ph-site specific detailed file |
| artmsIsEvidenceNewVersion | Check if a given evidencee file was generated by a new... |
| artmsIsSpeciesSupported | Check if a species is supported and available |
| artmsLeaveOnlyUniprotEntryID | Leave only the Entry ID from a typical full Uniprot IDs in a... |
| artmsMapUniprot2Entrez | Map GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot... |
| 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... |
| artmsProtein2SiteConversion | Converts the Protein ID column of the evidence file selected... |
| 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... |
| 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... |
