Files in samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R

.Rbuildignore

.github/.gitignore

.github/ISSUE_TEMPLATE/bug_report.md .github/ISSUE_TEMPLATE/feature_request.md

.github/workflows/R-CMD-check.yaml

.github/workflows/check-bioc.yml

.gitignore

DESCRIPTION

DaparToolshed.Rproj

NAMESPACE

NEWS.md R/AllGenerics.R R/DaparToolshed-filterFeaturesOneSE.R R/DaparToolshed.R R/DaparToolshed_QFeatures_Addons.R R/DaparToolshed_aggregate.R R/DaparToolshed_filter_Adjmat.R R/DaparToolshed_filter_qMetadata.R R/QFeatures_utils.R R/Workflows.old/Protein/mod_Protein.R R/Workflows.old/Protein/mod_Protein_Description.R R/Workflows.old/Protein/mod_Protein_Filtering.R R/Workflows.old/Protein/mod_Protein_Normalization.R

R/Workflows.old/workflow_list.txt

R/agregation.R R/design_utils.R R/doc-data.R R/example-data.R R/export_qfeatures.R R/get_pep_prot_cc.R R/global.R R/import_2_qfeatures.R R/iterative_agregation.R R/metacell.R R/mod_Agregation.R R/mod_Filtering.R R/mod_Protein.R R/mod_Protein_Description.R R/mod_Protein_Filtering.R R/mod_Protein_Normalization.R R/mod_buildDesign.R R/mod_build_qMetadata_FunctionFilter.R R/mod_convert.R R/mod_designExample.R R/mod_dl.R R/mod_ds_metacell.R R/mod_filtering_example.R R/mod_format_DT.R R/mod_helpPopover.R R/mod_infos_dataset.R R/mod_inputGroup.R R/mod_metacell_tree.R R/mod_open_dataset.R R/mod_open_demoDataset.R R/mod_query_metacell.R R/mod_settings.R R/mod_tracker.R R/palette.R R/pepa.R R/plot_metacell.R R/shinyValue.R R/utils.R R/zzz.R README.md

_pkgdown.yml

data/datalist

data/ft.rda

data/ft_na.rda

docs/404.html

docs/authors.html

docs/bootstrap-toc.css

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docs/news/index.html

docs/pkgdown.css

docs/pkgdown.js

docs/pkgdown.yml

docs/reference/Add_Item_to_Dataset.html

docs/reference/Base_Palette.html

docs/reference/DaparToolshed-aggregate.html

docs/reference/Example_Palette.html

docs/reference/GetProstarVersions.html

docs/reference/GraphPepProt_hc.html

docs/reference/Keep_Items_from_Dataset.html

docs/reference/LH0.html

docs/reference/LH0.lm.html

docs/reference/LH1.html

docs/reference/LH1.lm.html

docs/reference/Pipelines.html

docs/reference/ProstarVersions.html

docs/reference/QFeatures-accessors.html

docs/reference/QFeatures-excel.html

docs/reference/QFeatures-filtering-oneSE.html

docs/reference/QFeatures-supplementary-accessors.html

docs/reference/QFeatures-utils.html

docs/reference/ReplaceSpecialChars.html

docs/reference/Rplot001.png

docs/reference/UpdateqMetadata.html

docs/reference/adjacency-matrix-filter.html

docs/reference/checkClusterability.html

docs/reference/compute_t_tests.html

docs/reference/connected-components.html

docs/reference/connected_components.html

docs/reference/create-example.html

docs/reference/customChart.html

docs/reference/customExportMenu_HC.html

docs/reference/dapar_hc_ExportMenu.html

docs/reference/dapar_hc_chart.html

docs/reference/descriptive-statistics-plots-1.png

docs/reference/descriptive-statistics-plots.html

docs/reference/descriptive-statistics.html

docs/reference/descriptives-statistics-plots.html

docs/reference/diff_analysis_sam.html

docs/reference/differential-analysis.html

docs/reference/formatPHResults.html

docs/reference/fudge2LRT.html

docs/reference/getListNbValuesInLines.html

docs/reference/import-export-QFeatures.html

docs/reference/import-export-dataset.html

docs/reference/imputation.html

docs/reference/index.html

docs/reference/is.MV.html

docs/reference/is.OfType.html

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inst/CITATION

inst/NEWS.Rd

inst/extdata/ft-data-na.txt

inst/extdata/ft-data.txt

inst/extdata/ft-samples.txt

inst/extdata/ft.qf

inst/extdata/ft_na.qf

inst/extdata/utils/custom_mod_EDA.R inst/extdata/utils/custom_mod_convert.R inst/extdata/utils/custom_mod_exports.R inst/extdata/utils/custom_mod_openfile.R inst/extdata/utils/utils.R

inst/extdata/workflow/PipelineA/PipelineA.conf

inst/extdata/workflow/PipelineA/README.txt

inst/extdata/workflow/PipelineB/md/summary.html

inst/extdata/workflow/PipelineB/md/summary.md

inst/images/Ok.png

inst/images/Problem.png

inst/images/ds_metacell.png

inst/md/Agregation.md inst/md/Filtering.md

inst/md/Normalization.html

inst/md/Normalization.md inst/md/Pipeline.md inst/md/ProcessA.md inst/md/ProcessB.md inst/md/ProcessC.md inst/md/Protein.md inst/md/Protein_Description.md

inst/www/ds_corrmatrix.png

man/Add_Item_to_Dataset.Rd man/AggregateMetacell.Rd man/BuildAdjacencyMatrix.Rd man/BuildColumnToProteinDataset.Rd man/BuildMetaCell.Rd man/Children.Rd man/ConvertListToHtml.Rd man/CountPep.Rd man/DaparToolshed-aggregate.Rd man/DaparToolshed.Rd man/ExtendPalette.Rd man/GetColorsForConditions.Rd man/GetDetailedNbPeptides.Rd man/GetDetailedNbPeptidesUsed.Rd man/GetMetacell.Rd man/GetNbPeptidesUsed.Rd man/GetSoftAvailables.Rd man/GraphPepProt.Rd man/Keep_Items_from_Dataset.Rd man/LH0.Rd man/LH0.lm.Rd man/LH1.Rd man/LH1.lm.Rd man/Metacell_DIA_NN.Rd man/Metacell_maxquant.Rd man/Metacell_proline.Rd man/Parent.Rd man/Pipelines.Rd man/ProstarVersions.Rd man/QFeatures-accessors.Rd man/QFeatures-excel.Rd man/QFeatures-filtering-oneSE.Rd man/QFeatures-utils.Rd man/ReplaceSpecialChars.Rd man/adjacency-matrix-filter.Rd man/aggregateIter.Rd man/aggregateIterParallel.Rd man/aggregateMean.Rd man/aggregateSum.Rd man/aggregateTopn.Rd man/build-design.Rd man/buildGraph.Rd man/check.conditions.Rd man/check.design.Rd man/create-example.Rd man/design-example.Rd man/display.CC.visNet.Rd man/dl.Rd man/finalizeAggregation.Rd man/ft.Rd man/ft_na.Rd man/fudge2LRT.Rd man/get.pep.prot.cc.Rd man/getExtension.Rd man/getListNbValuesInLines.Rd man/getProteinsStats.Rd man/import-export-QFeatures.Rd man/inner.aggregate.iter.Rd man/inner.aggregate.topn.Rd man/inner.mean.Rd man/inner.sum.Rd man/is.OfType.Rd man/match.metacell.Rd man/metacell-plots.Rd man/metacell-tree.Rd man/mod_Agregation.Rd man/mod_Filtering.Rd man/mod_convert.Rd man/mod_filterExample.Rd man/mod_format_DT.Rd man/mod_helpPopover.Rd man/mod_infos_dataset.Rd man/mod_inputGroup.Rd man/mod_open_dataset.Rd man/mod_open_demo_dataset.Rd man/mod_settings.Rd man/my_hc_ExportMenu.Rd man/my_hc_chart.Rd man/nEmptyLines.Rd man/nonzero.Rd man/pepa.test.Rd man/pipeline-protein.Rd man/pkgs.require.Rd man/plotJitter.Rd man/plotJitter_rCharts.Rd man/qMetacell-filter.Rd man/q_metacell.Rd man/query-metacell.Rd man/query_qMetacell.Rd man/samLRT.Rd man/splitAdjacencyMat.Rd man/test.design.Rd man/tracking.Rd tests/testthat.R tests/testthat/test_utils.R vignettes/Prostar_UserManual.Rmd

vignettes/figs/GO_tab1.png

vignettes/figs/GO_tab2.png

vignettes/figs/GO_tab3.png

vignettes/figs/GO_tab4.png

vignettes/figs/Rcode.png

vignettes/figs/aggregation.png

vignettes/figs/agregation1.png

vignettes/figs/agregation2.png

vignettes/figs/anaDiff1.png

vignettes/figs/anaDiff2.png

vignettes/figs/anaDiff3.png

vignettes/figs/anaDiff4.png

vignettes/figs/anadiffsum.png

vignettes/figs/convert_convert.png

vignettes/figs/convert_dataID.png

vignettes/figs/convert_exp_featdata.png

vignettes/figs/convert_sampledata.png

vignettes/figs/convert_selectfile.png

vignettes/figs/cp4p-choice.png

vignettes/figs/cp4p-default.png

vignettes/figs/cp4p-ideal.png

vignettes/figs/cp4p-pb1.png

vignettes/figs/cp4p-pb2.png

vignettes/figs/defaultProstar1.png

vignettes/figs/demomode.png

vignettes/figs/desc_CVDist.png

vignettes/figs/desc_CVDist_ZoomIn.png

vignettes/figs/desc_CVDist_ZoomOut.png

vignettes/figs/desc_PCA.png

vignettes/figs/desc_boxplot.png

vignettes/figs/desc_corrmatrix.png

vignettes/figs/desc_density.png

vignettes/figs/desc_fdata.png

vignettes/figs/desc_heatmap.png

vignettes/figs/desc_intdistrib.png

vignettes/figs/desc_missValues.png

vignettes/figs/desc_pdata.png

vignettes/figs/desc_quantiData.png

vignettes/figs/desc_varDist.png

vignettes/figs/desc_violinplot.png

vignettes/figs/descstat-overview.png

vignettes/figs/equiv-non-fig.txt

vignettes/figs/export.png

vignettes/figs/exportReport.png

vignettes/figs/fdr-thresh.png

vignettes/figs/filter1.png

vignettes/figs/filter2.png

vignettes/figs/filter3.png

vignettes/figs/home.png

vignettes/figs/hp.png

vignettes/figs/imputation.png

vignettes/figs/load-pep.png

vignettes/figs/load-prot.png

vignettes/figs/logSession.png

vignettes/figs/normalisation.png

vignettes/figs/open_msnset.png

vignettes/figs/peptide-basicImputation.png

vignettes/figs/peptide-imp4p.png

vignettes/figs/protein-MEC.png

vignettes/figs/protein-POV.png

vignettes/figs/pushpval.png

samWieczorek/DAPAR2 documentation built on Oct. 15, 2023, 1:45 p.m.

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samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R

Files in samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R

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samWieczorek/DAPAR2 Tools for the Differential Analysis of Proteins Abundance with R

Files in samWieczorek/DAPAR2 Tools for the Differential Analysis of Proteins Abundance with R

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samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R

Files in samWieczorek/DAPAR2
Tools for the Differential Analysis of Proteins Abundance with R