Package: artMS 1.25.0

David Jimenez-Morales

artMS: Analytical R tools for Mass Spectrometry

artMS provides a set of tools for the analysis of proteomics label-free datasets. It takes as input the MaxQuant search result output (evidence.txt file) and performs quality control, relative quantification using MSstats, downstream analysis and integration. artMS also provides a set of functions to re-format and make it compatible with other analytical tools, including, SAINTq, SAINTexpress, Phosfate, and PHOTON. Check [http://artms.org](http://artms.org) for details.

Authors:David Jimenez-Morales [aut, cre], Alexandre Rosa Campos [aut, ctb], John Von Dollen [aut], Nevan Krogan [aut], Danielle Swaney [aut, ctb]

artMS_1.25.0.tar.gz
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artMS.pdf |artMS.html✨
artMS/json (API)
NEWS

# Install 'artMS' in R:
install.packages('artMS', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Peer review:

Bug tracker:https://github.com/biodavidjm/artms/issues

Datasets:

On BioConductor:artMS-1.25.0(bioc 3.21)artMS-1.24.0(bioc 3.20)

proteomicsdifferentialexpressionbiomedicalinformaticssystemsbiologymassspectrometryannotationqualitycontrolgenesetenrichmentclusteringnormalizationimmunooncologymultiplecomparisonanalysisanalyticalap-msbioconductorbioinformaticsmass-spectrometryphosphoproteomicspost-translational-modificationquantitative-analysis

6.37 score 14 stars 12 scripts 206 downloads 2 mentions 33 exports 136 dependencies

Last updated 2 months agofrom:10716cd4ac. Checks:OK: 7. Indexed: yes.

TargetResultDate
Doc / VignettesOKDec 14 2024
R-4.5-winOKDec 14 2024
R-4.5-linuxOKDec 14 2024
R-4.4-winOKDec 14 2024
R-4.4-macOKDec 14 2024
R-4.3-winOKDec 14 2024
R-4.3-macOKDec 14 2024

Exports:artmsAnalysisQuantificationsartmsAnnotateSpecieartmsAnnotationUniprotartmsAvgIntensityRTartmsChangeColumnNameartmsConvertMetabolomicsartmsDataPlotsartmsEnrichLog2fcartmsEnrichProfilerartmsEvidenceToSaintExpressartmsEvidenceToSAINTqartmsFilterEvidenceContaminantsartmsGeneratePhSiteExtendedartmsIsEvidenceNewVersionartmsIsSpeciesSupportedartmsLeaveOnlyUniprotEntryIDartmsMapUniprot2EntrezartmsMergeEvidenceAndKeysartmsMsstatsSummaryartmsPhosfateOutputartmsPhotonOutputartmsPlotHeatmapQuantartmsProtein2SiteConversionartmsQualityControlEvidenceBasicartmsQualityControlEvidenceExtendedartmsQualityControlMetabolomicsartmsQualityControlSummaryExtendedartmsQuantificationartmsResultsWideartmsSILACtoLongartmsSpectralCountsartmsVolcanoPlotartmsWriteConfigYamlFile

Dependencies:ade4AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootbslibcachemcaToolscheckmatecirclizecliclustercolorspacecorrplotcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagetoptggdendroggplot2ggrepelGlobalOptionsgluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4log4rmagrittrmarrayMASSMatrixmemoisemgcvmimeminqaMSstatsMSstatsConvertmunsellnlmenloptropensslopenxlsxorg.Hs.eg.dbpheatmappillarpixmappkgconfigplogrplotlyplyrpngpreprocessCorepromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownRSQLiteS4VectorssassscalessegmentedseqinrshapespstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsUpSetRutf8vctrsVennDiagramviridisLitewithrxfunXVectoryamlzipzlibbioc

artMS: Analytical R Tools for Mass Spectrometry

David Jimenez-Morales

Rendered fromartMS_vignette.Rmdusingknitr::rmarkdownon Dec 14 2024.

Last update: 2021-07-14
Started: 2018-06-13

Readme and manuals

Help Manual

Help pageTopics
artMS configuration templateartms_config
CORUM Protein Complexes database use for complex enrichment analysisartms_data_corum_mito_database
LPN PATHOGEN: Legionella pneumophila subsp. pneumophila (strain Philadelphia 1 / ATCC 33152 / DSM 7513) UNIPROT IDSartms_data_pathogen_LPN
TB PATHOGEN: Mycobacterium tuberculosis (strain ATCC 35801 / TMC 107 / Erdman) UNIPROTS IDSartms_data_pathogen_TB
artMS configuration for the available PH datasetartms_data_ph_config
Contrast example for the PH datasetartms_data_ph_contrast
Evidence file exampleartms_data_ph_evidence
Keys File Exampleartms_data_ph_keys
MSstats modelQC exampleartms_data_ph_msstats_modelqc
MSstats results exampleartms_data_ph_msstats_results
Random data setartms_data_randomDF
Analysis of the Relative QuantificationsartmsAnalysisQuantifications
Adding a column with the species nameartmsAnnotateSpecie
Annotate table with Gene Symbol and Name based on Uniprot ID(s)artmsAnnotationUniprot
Summarize average intensity and retention time per proteinartmsAvgIntensityRT
Change a specific column name in a given data.frameartmsChangeColumnName
Convert Markview Metabolomics file (alignment table) into a artMS compatible formatartmsConvertMetabolomics
Individual Normalized abundance dot plots for every proteinartmsDataPlots
Enrichment of changes in protein abundance or PTMsartmsEnrichLog2fc
Enrichment analysis using GprofileRartmsEnrichProfiler
MaxQuant evidence file to SAINTexpress formatartmsEvidenceToSaintExpress
MaxQuant evidence file to SAINTq formatartmsEvidenceToSAINTq
Remove contaminants and empty proteins from the MaxQuant evidence fileartmsFilterEvidenceContaminants
Generate ph-site specific detailed fileartmsGeneratePhSiteExtended
Check if a given evidencee file was generated by a new version of MaxQuant (v>1)artmsIsEvidenceNewVersion
Check if a species is supported and availableartmsIsSpeciesSupported
Leave only the Entry ID from a typical full Uniprot IDs in a given columnartmsLeaveOnlyUniprotEntryID
Map GENE SYMBOL, NAME, AND ENTREZID to a vector of Uniprot IDSartmsMapUniprot2Entrez
Merge evidence.txt (or summary.txt) with keys.txt filesartmsMergeEvidenceAndKeys
Summarize the MSStats results and data quantificationartmsMsstatsSummary
Generate Phosfate Input fileartmsPhosfateOutput
Generate PHOTON Input fileartmsPhotonOutput
Outputs a heatmap of the MSStats results created using the log2fold changesartmsPlotHeatmapQuant
Converts the Protein ID column of the evidence file selected by the user to mod-site-specific notation: 'ProteinID' to 'ProteinID_AAnumber' notationartmsProtein2SiteConversion
Quality Control analysis of the MaxQuant evidence fileartmsQualityControlEvidenceBasic
Extended Quality Control of the MaxQuant evidence.txt fileartmsQualityControlEvidenceExtended
Quality Control analysis of the evidence-like metabolomics datasetartmsQualityControlMetabolomics
Quality Control of the MaxQuant summary.txt fileartmsQualityControlSummaryExtended
Relative quantification using MSstatsartmsQuantification
Reshape the MSstats results file from long to wide formatartmsResultsWide
Convert the SILAC evidence file to MSstats formatartmsSILACtoLong
Outputs the spectral counts from the MaxQuant evidence file.artmsSpectralCounts
Volcano plot (log2fc / pvalues)artmsVolcanoPlot
Write out a template file of the artMS configuration file (yaml)artmsWriteConfigYamlFile