Files in biodavidjm/artMS
Analytical R tools for Mass Spectrometry

.Rbuildignore
.gitignore
.travis.yml
DESCRIPTION
LICENSE
NAMESPACE
NEWS
R/MSstats_functions.R R/analysisQuantifications.R R/annotations.R R/avg_intensity_RT.R R/checkIfFile.R R/data.R R/enrichments.R R/evidenceToSAINTqFormat.R R/evidenceToSaintExpressFormat.R R/getMSstatsformat.R R/main.R R/metabolomics.R R/msstat_summary.R R/otherApps.R R/plots.R R/protein2SiteConversion.R R/qualityControlEvidenceBasic.R R/qualityControlEvidenceExtended.R R/qualityControlMetabolomics.R R/qualityControlSummaryExtended.R R/runMSstats.R R/writeExtras.R README.md
_pkgdown.yml
data/artms_config.RData
data/artms_data_corum_mito_database.RData
data/artms_data_pathogen_LPN.RData
data/artms_data_pathogen_TB.RData
data/artms_data_ph_config.RData
data/artms_data_ph_contrast.RData
data/artms_data_ph_evidence.RData
data/artms_data_ph_keys.RData
data/artms_data_ph_msstats_modelqc.RData
data/artms_data_ph_msstats_results.RData
data/artms_data_randomDF.RData
docs/404.html
docs/LICENSE-text.html
docs/articles/artMS_vignette.html
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-1.png
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docs/articles/artMS_vignette_files/header-attrs-2.9/header-attrs.js
docs/articles/index.html
docs/authors.html
docs/bootstrap-toc.css
docs/bootstrap-toc.js
docs/docsearch.css
docs/docsearch.js
docs/index.html
docs/link.svg
docs/pkgdown.css
docs/pkgdown.js
docs/pkgdown.yml
docs/reference/Rplot001.png
docs/reference/Rplot002.png
docs/reference/artmsAnalysisQuantifications.html
docs/reference/artmsAnnotateSpecie.html
docs/reference/artmsAnnotationUniprot.html
docs/reference/artmsAvgIntensityRT.html
docs/reference/artmsChangeColumnName.html
docs/reference/artmsConvertMetabolomics.html
docs/reference/artmsDataPlots.html
docs/reference/artmsEnrichLog2fc.html
docs/reference/artmsEnrichProfiler.html
docs/reference/artmsEvidenceToSAINTq.html
docs/reference/artmsEvidenceToSaintExpress.html
docs/reference/artmsFilterEvidenceContaminants.html
docs/reference/artmsGeneratePhSiteExtended.html
docs/reference/artmsIsEvidenceNewVersion.html
docs/reference/artmsIsSpeciesSupported.html
docs/reference/artmsLeaveOnlyUniprotEntryID.html
docs/reference/artmsMapUniprot2Entrez.html
docs/reference/artmsMergeEvidenceAndKeys.html
docs/reference/artmsMsstatsSummary.html
docs/reference/artmsPhosfateOutput.html
docs/reference/artmsPhotonOutput.html
docs/reference/artmsPlotHeatmapQuant-1.png
docs/reference/artmsPlotHeatmapQuant.html
docs/reference/artmsProtein2SiteConversion.html
docs/reference/artmsQualityControlEvidenceBasic-1.png
docs/reference/artmsQualityControlEvidenceBasic-2.png
docs/reference/artmsQualityControlEvidenceBasic.html
docs/reference/artmsQualityControlEvidenceExtended.html
docs/reference/artmsQualityControlMetabolomics.html
docs/reference/artmsQualityControlSummaryExtended.html
docs/reference/artmsQuantification.html
docs/reference/artmsResultsWide.html
docs/reference/artmsSILACtoLong.html
docs/reference/artmsSpectralCounts.html
docs/reference/artmsVolcanoPlot-1.png
docs/reference/artmsVolcanoPlot.html
docs/reference/artmsWriteConfigYamlFile.html
docs/reference/artms_config.html
docs/reference/artms_data_corum_mito_database.html
docs/reference/artms_data_pathogen_LPN.html
docs/reference/artms_data_pathogen_TB.html
docs/reference/artms_data_ph_config.html
docs/reference/artms_data_ph_contrast.html
docs/reference/artms_data_ph_evidence.html
docs/reference/artms_data_ph_keys.html
docs/reference/artms_data_ph_msstats_modelqc.html
docs/reference/artms_data_ph_msstats_results.html
docs/reference/artms_data_randomDF.html
docs/reference/index.html
docs/sitemap.xml
inst/extdata/artms_config.yaml
inst/extdata/createData.R inst/extdata/manuscriptCaseStudies.R man/artmsAnalysisQuantifications.Rd man/artmsAnnotateSpecie.Rd man/artmsAnnotationUniprot.Rd man/artmsAvgIntensityRT.Rd man/artmsChangeColumnName.Rd man/artmsConvertMetabolomics.Rd man/artmsDataPlots.Rd man/artmsEnrichLog2fc.Rd man/artmsEnrichProfiler.Rd man/artmsEvidenceToSAINTq.Rd man/artmsEvidenceToSaintExpress.Rd man/artmsFilterEvidenceContaminants.Rd man/artmsGeneratePhSiteExtended.Rd man/artmsIsEvidenceNewVersion.Rd man/artmsIsSpeciesSupported.Rd man/artmsLeaveOnlyUniprotEntryID.Rd man/artmsMapUniprot2Entrez.Rd man/artmsMergeEvidenceAndKeys.Rd man/artmsMsstatsSummary.Rd man/artmsPhosfateOutput.Rd man/artmsPhotonOutput.Rd man/artmsPlotHeatmapQuant.Rd man/artmsProtein2SiteConversion.Rd man/artmsQualityControlEvidenceBasic.Rd man/artmsQualityControlEvidenceExtended.Rd man/artmsQualityControlMetabolomics.Rd man/artmsQualityControlSummaryExtended.Rd man/artmsQuantification.Rd man/artmsResultsWide.Rd man/artmsSILACtoLong.Rd man/artmsSpectralCounts.Rd man/artmsVolcanoPlot.Rd man/artmsWriteConfigYamlFile.Rd man/artms_config.Rd man/artms_data_corum_mito_database.Rd man/artms_data_pathogen_LPN.Rd man/artms_data_pathogen_TB.Rd man/artms_data_ph_config.Rd man/artms_data_ph_contrast.Rd man/artms_data_ph_evidence.Rd man/artms_data_ph_keys.Rd man/artms_data_ph_msstats_modelqc.Rd man/artms_data_ph_msstats_results.Rd man/artms_data_randomDF.Rd tests/testthat.R tests/testthat/test-evidence.R vignettes/artMS_vignette.R vignettes/artMS_vignette.Rmd
biodavidjm/artMS documentation built on July 7, 2023, 12:24 p.m.