|
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 |