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
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-2.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-3.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-4.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-5.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-4-6.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-1.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-2.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-3.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-4.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-5.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-6.png
docs/articles/artMS_vignette_files/figure-html/unnamed-chunk-6-7.png
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
