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

artms_analysisQuantificationsAnalysis of the Relative Quantification
artms_annotateSpecieAdding a column with the species name
artms_annotationUniprotAnnotate table with Gene Symbol and Name based on Uniprot...
artms_avg_intensity_RTSummarize average intensity and retention time per protein
artms_changeColumnNameChange a specific column name in a given data.frame
artms_configartMS configuration template
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
artms_dataPlotsIndividual Normalized abundance dot plots for every protein
artms_data_randomDFRandom data set
artms_enrichLog2fcEnrichment of changes in protein abundance or PTMs
artms_enrichProfilerEnrichment analysis using GprofileR
artms_evidenceToSaintExpressFormatMaxQuant evidence file to SAINTexpress format
artms_evidenceToSAINTqFormatMaxQuant evidence file to SAINTq format
artms_filterEvidenceContaminantsRemove contaminants and empty proteins from the MaxQuant...
artms_generatePhSiteExtendedGenerate ph-site specific detailed file
artms_isEvidenceNewVersionCheck if a given evidencee file was generated by a new...
artmsMapUniprot2EntrezMap GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot...
artms_mergeEvidenceAndKeysMerge evidence.txt (or summary.txt) with keys.txt files
artms_msstats_summarySummarize the MSStats results and data quantification
artmsPhosfateOutputGenerate Phosfate Input file
artmsPhotonOutputGenerate PHOTON Input file
artms_plotHeatmapQuantOutputs a heatmap of the MSStats results created using the...
artms_proteinToSiteConversionConverts the 'Proteins' column of the evidence file to...
artms_qualityControlEvidenceBasicQuality Control analysis of the MaxQuant evidence file
artms_qualityControlEvidenceExtendedExtended Quality Control of the MaxQuant evidence.txt file
artms_qualityControlSummaryExtendedQuality Control of the MaxQuant summary.txt file
artms_quantificationRelative quantification using MSstats
artms_replicatePlotsCreate the replicate plots based on the pairings from the...
artms_resultsWideReshape the MSstats results file from long to wide format
artms_SILACtoLongConvert the SILAC evidence file to MSstats format
artms_spectralCountsOutputs the spectral counts from the MaxQuant evidence file.
artms_volcanoPlotVolcano plot (log2fc / pvalues)
artms_writeConfigYamlFileWrite out a template file of the artMS configuration file...
kroganlab/artMS documentation built on Oct. 15, 2018, 9:17 p.m.