Man pages for biodavidjm/artMS
Analytical R tools for Mass Spectrometry

artmsAnalysisQuantificationsAnalysis of the Relative Quantifications
artmsAnnotateSpecieAdding a column with the species name
artmsAnnotationUniprotAnnotate table with Gene Symbol and Name based on Uniprot...
artmsAvgIntensityRTSummarize average intensity and retention time per protein
artmsChangeColumnNameChange a specific column name in a given data.frame
artms_configartMS configuration template
artmsConvertMetabolomicsConvert Markview Metabolomics file (alignment table) into a...
artms_data_corum_mito_databaseCORUM Protein Complexes database use for complex enrichment...
artms_data_pathogen_LPNLPN PATHOGEN: Legionella pneumophila subsp. pneumophila...
artms_data_pathogen_TBTB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 /...
artms_data_ph_evidenceEvidence file example
artms_data_ph_keysKeys File Example
artms_data_ph_msstats_resultsMSstats results file example
artmsDataPlotsIndividual Normalized abundance dot plots for every protein
artms_data_randomDFRandom data set
artmsEnrichLog2fcEnrichment of changes in protein abundance or PTMs
artmsEnrichProfilerEnrichment analysis using GprofileR
artmsEvidenceToSaintExpressMaxQuant evidence file to SAINTexpress format
artmsEvidenceToSAINTqMaxQuant evidence file to SAINTq format
artmsFilterEvidenceContaminantsRemove contaminants and empty proteins from the MaxQuant...
artmsGeneratePhSiteExtendedGenerate ph-site specific detailed file
artmsIsEvidenceNewVersionCheck if a given evidencee file was generated by a new...
artmsMapUniprot2EntrezMap GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot...
artmsMergeEvidenceAndKeysMerge evidence.txt (or summary.txt) with keys.txt files
artmsMsstatsSummarySummarize the MSStats results and data quantification
artmsPhosfateOutputGenerate Phosfate Input file
artmsPhotonOutputGenerate PHOTON Input file
artmsPlotHeatmapQuantOutputs a heatmap of the MSStats results created using the...
artmsProtein2SiteConversionConverts the 'Proteins' column of the evidence file to...
artmsQualityControlEvidenceBasicQuality Control analysis of the MaxQuant evidence file
artmsQualityControlEvidenceExtendedExtended Quality Control of the MaxQuant evidence.txt file
artmsQualityControlMetabolomicsQuality Control analysis of the evidence-like metabolomics...
artmsQualityControlSummaryExtendedQuality Control of the MaxQuant summary.txt file
artmsQuantificationRelative quantification using MSstats
artmsReplicatePlotsCreate the replicate plots based on the pairings from the...
artmsResultsWideReshape the MSstats results file from long to wide format
artmsSILACtoLongConvert the SILAC evidence file to MSstats format
artmsSpectralCountsOutputs the spectral counts from the MaxQuant evidence file.
artmsVolcanoPlotVolcano plot (log2fc / pvalues)
artmsWriteConfigYamlFileWrite out a template file of the artMS configuration file...
biodavidjm/artMS documentation built on Nov. 18, 2018, 6:25 p.m.