| 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 |