Files in Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications

.Rbuildignore

.github/workflows/dry-run-build.yml

.gitignore

.travis.yml

DESCRIPTION

NAMESPACE

R/MSstatsPTM.R R/RcppExports.R R/converters.R R/dataDoc.R R/dataProcessPlotsPTM.R R/dataSummarizationPTM.R R/dataSummarizationPTM_TMT.R R/designSampleSizePTM.R R/groupComparisonPTM.R R/groupComparisonPlotsPTM.R R/locatePTM.R R/msstatsptm-package.R R/utils_checks.R R/utils_converters.R R/utils_dataProcessPlots.R R/utils_groupComparison.R R/utils_groupComparisonPlots.R README.md

_pkgdown.yml

data/fragpipe_annotation.rda

data/fragpipe_annotation_protein.rda

data/fragpipe_input.rda

data/fragpipe_input_protein.rda

data/maxq_lf_annotation.rda

data/maxq_lf_evidence.rda

data/maxq_tmt_annotation.rda

data/maxq_tmt_evidence.rda

data/pd_annotation.rda

data/pd_psm_input.rda

data/pd_testing_output.rda

data/raw.input.rda

data/raw.input.tmt.rda

data/spectronaut_annotation.rda

data/spectronaut_input.rda

data/summary.data.rda

data/summary.data.tmt.rda

docs/404.html

docs/LICENSE.html

docs/articles/MSstatsPTM_LabelFree_Workflow.html

docs/articles/MSstatsPTM_LabelFree_Workflow_files/figure-html/heatmap-1.png

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docs/articles/MSstatsPTM_LabelFree_Workflow_files/header-attrs-2.7/header-attrs.js

docs/articles/MSstatsPTM_LabelFree_Workflow_files/header-attrs-2.8/header-attrs.js

docs/articles/MSstatsPTM_TMT_Workflow.html

docs/articles/MSstatsPTM_TMT_Workflow_files/figure-html/meatmap-1.png

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docs/articles/MSstatsPTM_TMT_Workflow_files/figure-html/profileplot-1.png

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docs/articles/MSstatsPTM_TMT_Workflow_files/figure-html/qcplot-1.png

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docs/articles/MSstatsPTM_TMT_Workflow_files/header-attrs-2.7/header-attrs.js

docs/articles/MSstatsPTM_TMT_Workflow_files/header-attrs-2.8/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/MSstatsPTM.html

docs/reference/MaxQtoMSstatsPTMFormat.html

docs/reference/ProgenesistoMSstatsPTMFormat.html

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docs/reference/Rplot017.png

docs/reference/Rplot018.png

docs/reference/SpectronauttoMSstatsPTMFormat.html

docs/reference/annotSite.html

docs/reference/dataProcessPlotsPTM-1.png

docs/reference/dataProcessPlotsPTM-2.png

docs/reference/dataProcessPlotsPTM-3.png

docs/reference/dataProcessPlotsPTM.html

docs/reference/dataSummarizationPTM.html

docs/reference/dataSummarizationPTM_TMT.html

docs/reference/globalConverterPTM.html

docs/reference/groupComparisonPTM.html

docs/reference/groupComparisonPlotsPTM-1.png

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docs/reference/groupComparisonPlotsPTM.html

docs/reference/index.html

docs/reference/locateMod.html

docs/reference/locatePTM.html

docs/reference/raw.input.html

docs/reference/raw.input.tmt.html

docs/reference/summary.data.html

docs/reference/summary.data.tmt.html

docs/reference/tidyFasta.html

inst/CITATION

inst/NEWS.rd

inst/extdata/O13297.fasta

inst/extdata/maxq_lf_fasta.fasta

inst/extdata/maxq_tmt_fasta.fasta

inst/extdata/metamorpheus_fasta.fasta

inst/extdata/pd_fasta.fasta

inst/extdata/pd_with_proteome.fasta

inst/extdata/spectronaut_fasta.fasta

inst/tinytest/raw_data/Fragpipe/MSstats.csv

inst/tinytest/raw_data/Fragpipe/experiment_annotation.tsv

inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaks.tsv

inst/tinytest/raw_data/Metamorpheus/AllQuantifiedPeaksGlobalProteome.tsv

inst/tinytest/raw_data/Metamorpheus/ExperimentalDesign.tsv

inst/tinytest/raw_data/Metamorpheus/ExperimentalDesignGlobalProteome.tsv

inst/tinytest/raw_data/PD/pd-ptm-annot.csv

inst/tinytest/raw_data/PD/pd-ptm-input.csv

inst/tinytest/raw_data/PD/protein-annot.csv

inst/tinytest/raw_data/PD/protein-input.csv

inst/tinytest/raw_data/Progenesis/phospho_annotation.csv

inst/tinytest/raw_data/Progenesis/progenesis_peptide.csv

src/.gitignore

src/RcppExports.cpp

src/model_adjustment.cpp

tests/testthat.R tests/testthat/test_dataProcessPlotsPTM.R tests/tinytest.R

vignettes/.gitignore

vignettes/MSstatsPTM_LabelFree_Workflow.Rmd vignettes/MSstatsPTM_TMT_Workflow.Rmd

Vitek-Lab/MSstatsPTM documentation built on Sept. 26, 2024, 9:28 p.m.

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Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications

Files in Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications

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Vitek-Lab/MSstatsPTM Statistical Characterization of Post-translational Modifications

Files in Vitek-Lab/MSstatsPTM Statistical Characterization of Post-translational Modifications

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Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications

Files in Vitek-Lab/MSstatsPTM
Statistical Characterization of Post-translational Modifications