Package: artMS 1.23.0
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:
artMS_1.23.0.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')) |
Bug tracker:https://github.com/biodavidjm/artms/issues
- 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
On BioConductor:artMS-1.23.0(bioc 3.20)artMS-1.22.0(bioc 3.19)
Last updated 2 months agofrom:1c0254127c
Exports:artmsAnalysisQuantificationsartmsAnnotateSpecieartmsAnnotationUniprotartmsAvgIntensityRTartmsChangeColumnNameartmsConvertMetabolomicsartmsDataPlotsartmsEnrichLog2fcartmsEnrichProfilerartmsEvidenceToSaintExpressartmsEvidenceToSAINTqartmsFilterEvidenceContaminantsartmsGeneratePhSiteExtendedartmsIsEvidenceNewVersionartmsIsSpeciesSupportedartmsLeaveOnlyUniprotEntryIDartmsMapUniprot2EntrezartmsMergeEvidenceAndKeysartmsMsstatsSummaryartmsPhosfateOutputartmsPhotonOutputartmsPlotHeatmapQuantartmsProtein2SiteConversionartmsQualityControlEvidenceBasicartmsQualityControlEvidenceExtendedartmsQualityControlMetabolomicsartmsQualityControlSummaryExtendedartmsQuantificationartmsResultsWideartmsSILACtoLongartmsSpectralCountsartmsVolcanoPlotartmsWriteConfigYamlFile
Dependencies:ade4AnnotationDbiaskpassbackportsbase64encBiobaseBiocGenericsBiostringsbitbit64bitopsblobbootbslibcachemcaToolscheckmatecirclizecliclustercolorspacecorrplotcpp11crayoncrosstalkcurldata.tableDBIdigestdplyrevaluatefansifarverfastmapfontawesomeformatRfsfutile.loggerfutile.optionsgenericsGenomeInfoDbGenomeInfoDbDatagetoptggdendroggplot2ggrepelGlobalOptionsgluegplotsgridExtragtablegtoolshighrhtmltoolshtmlwidgetshttrIRangesisobandjquerylibjsonliteKEGGRESTKernSmoothknitrlabelinglambda.rlaterlatticelazyevallifecyclelimmalme4log4rmagrittrmarrayMASSMatrixmemoisemgcvmimeminqaMSstatsMSstatsConvertmunsellnlmenloptropensslopenxlsxorg.Hs.eg.dbpheatmappillarpixmappkgconfigplogrplotlyplyrpngpreprocessCorepromisespurrrR6rappdirsRColorBrewerRcppRcppArmadilloRcppEigenrlangrmarkdownRSQLiteS4VectorssassscalessegmentedseqinrshapespstatmodstringistringrsurvivalsystibbletidyrtidyselecttinytexUCSC.utilsUpSetRutf8vctrsVennDiagramviridisLitewithrxfunXVectoryamlzipzlibbioc