Files in NicWir/VisomX
User-Friendly and Comprehensive Analysis and Visualization of Omics Data
.Rbuildignore
.Renviron
.github/.gitignore
.github/workflows/check-bioc.yml
.github/workflows/pkgdown.yaml
.gitignore
DESCRIPTION
LICENSE.md
NAMESPACE
R/general_misc_utils.R
R/map_visualization.R
R/metabolomics_computation.R
R/metabolomics_plots.R
R/proteomics_computation.R
R/proteomics_plots.R
R/transcriptomics_computation.R
R/transcriptomics_plots.R
README.md
VisomX.Rproj
_pkgdown.yml
doc/vignette_proteomics.R
doc/vignette_proteomics.Rmd
doc/vignette_proteomics.html
docs/404.html
docs/LICENSE.html
docs/articles/index.html
docs/articles/vignette_proteomics.html
docs/articles/vignette_proteomics_files/figure-html/PlotBar-1.png
docs/articles/vignette_proteomics_files/figure-html/PlotBarFC-1.png
docs/articles/vignette_proteomics_files/figure-html/correlation_heatmap-1.png
docs/articles/vignette_proteomics_files/figure-html/correlation_heatmap_all-1.png
docs/articles/vignette_proteomics_files/figure-html/coverage-1.png
docs/articles/vignette_proteomics_files/figure-html/density-1.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_custom_dn-1.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_custom_dn-2.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_custom_up-1.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_custom_up-2.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_kegg-1.png
docs/articles/vignette_proteomics_files/figure-html/enrichment_kegg-2.png
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docs/articles/vignette_proteomics_files/figure-html/loadingsPlot-1.png
docs/articles/vignette_proteomics_files/figure-html/meanSDplot1-1.png
docs/articles/vignette_proteomics_files/figure-html/meanSDplot2-1.png
docs/articles/vignette_proteomics_files/figure-html/missval-1.png
docs/articles/vignette_proteomics_files/figure-html/missval2-1.png
docs/articles/vignette_proteomics_files/figure-html/norm-1.png
docs/articles/vignette_proteomics_files/figure-html/numbers-1.png
docs/articles/vignette_proteomics_files/figure-html/plot_pca_1_2-1.png
docs/articles/vignette_proteomics_files/figure-html/plot_pca_1_3-1.png
docs/articles/vignette_proteomics_files/figure-html/screeplot-1.png
docs/articles/vignette_proteomics_files/figure-html/volcano-1.png
docs/authors.html
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js
docs/deps/bootstrap-5.2.2/bootstrap.bundle.min.js.map
docs/deps/bootstrap-5.2.2/bootstrap.min.css
docs/deps/data-deps.txt
docs/deps/jquery-3.6.0/jquery-3.6.0.js
docs/deps/jquery-3.6.0/jquery-3.6.0.min.js
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docs/reference/Intersect.html
docs/reference/Perform.permutation.html
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docs/reference/dot-onAttach.html
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docs/reference/filter_missval.html
docs/reference/flux_to_map.html
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docs/reference/manual_impute.html
docs/reference/meanSdPlot.html
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docs/reference/met.GetFC.html
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docs/reference/met.PLSDA.Permut.html
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docs/reference/met.plot_ImpVar.html
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docs/reference/met.plot_PLS3DLoading.html
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docs/reference/pathway_enrich.html
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docs/reference/png_to_gif.html
docs/reference/prot.add_rejections.html
docs/reference/prot.boxplot_intensity.html
docs/reference/prot.filter_missing.html
docs/reference/prot.get_kegg_pathways.html
docs/reference/prot.get_results.html
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docs/reference/svg_to_pdf.html
docs/reference/svg_to_png.html
docs/reference/theme_DEP1.html
docs/reference/theme_DEP2.html
docs/search.json
docs/sitemap.xml
inst/BioCyc_pathways_KT2440.txt
inst/Report_Met.Rmd
inst/Report_Met_TestNorm.Rmd
inst/Report_Prot.Rmd
inst/Report_RNA.Rmd
inst/prot_KT2440_glc_ac_LB.txt
man/Get.bwss.Rd
man/Intersect.Rd
man/Perform.permutation.Rd
man/Setdiff.Rd
man/Union.Rd
man/colFmt.Rd
man/delete_prefix.Rd
man/dot-onAttach.Rd
man/fast.write.csv.Rd
man/filter_missval.Rd
man/flux_to_map.Rd
man/get_prefix.Rd
man/make_se.Rd
man/manual_impute.Rd
man/meanSdPlot.Rd
man/met.ANOVA.Anal.Rd
man/met.FC.Anal.Rd
man/met.FilterVariable.Rd
man/met.GetFC.Rd
man/met.GetTtestRes.Rd
man/met.PCA.Anal.Rd
man/met.PLSDA.CV.Rd
man/met.PLSDA.Permut.Rd
man/met.PLSR.Anal.Rd
man/met.PerformFeatureFilter.Rd
man/met.PreparePrenormData.Rd
man/met.SanityCheck.Rd
man/met.Ttests.Anal.Rd
man/met.UpdateData.Rd
man/met.impute.Rd
man/met.initialize.Rd
man/met.normalize.Rd
man/met.plot_ANOVA.Rd
man/met.plot_CorrHeatMap_Features.Rd
man/met.plot_CorrHeatMap_Samples.Rd
man/met.plot_FeatureNormSummary.Rd
man/met.plot_ImpVar.Rd
man/met.plot_PCA2DLoading.Rd
man/met.plot_PCA2DScore.Rd
man/met.plot_PCA3DLoading.Rd
man/met.plot_PCA3DScore.Rd
man/met.plot_PCAScree.Rd
man/met.plot_PLS.Crossvalidation.Rd
man/met.plot_PLS.Permutation.Rd
man/met.plot_PLS2DLoading.Rd
man/met.plot_PLS2DScore.Rd
man/met.plot_PLS3DLoading.Rd
man/met.plot_PLS3DScore.Rd
man/met.plot_PLSImpScatter.Rd
man/met.plot_PLS_Imp.Rd
man/met.plot_SampleNormSummary.Rd
man/met.plot_detect.Rd
man/met.plot_heatmap.Rd
man/met.plot_missval.Rd
man/met.plot_volcano.Rd
man/met.print_PCA3DLoading.Rd
man/met.print_PCA3DScore.Rd
man/met.print_PLS3DLoading.Rd
man/met.print_PLS3DScore.Rd
man/met.read_data.Rd
man/met.report.Rd
man/met.report_test_normalization.Rd
man/met.test_normalization.Rd
man/met.workflow.Rd
man/pathway_enrich.Rd
man/plot_coverage.Rd
man/png_to_gif.Rd
man/prot.add_rejections.Rd
man/prot.boxplot_intensity.Rd
man/prot.filter_missing.Rd
man/prot.get_kegg_pathways.Rd
man/prot.get_results.Rd
man/prot.impute.Rd
man/prot.make_unique.Rd
man/prot.normalize_vsn.Rd
man/prot.pca.Rd
man/prot.plot_bar.Rd
man/prot.plot_corrheatmap.Rd
man/prot.plot_density.Rd
man/prot.plot_detect.Rd
man/prot.plot_enrichment.Rd
man/prot.plot_heatmap.Rd
man/prot.plot_heatmap_all.Rd
man/prot.plot_imputation.Rd
man/prot.plot_loadings.Rd
man/prot.plot_missval.Rd
man/prot.plot_numbers.Rd
man/prot.plot_pca.Rd
man/prot.plot_screeplot.Rd
man/prot.plot_upset.Rd
man/prot.plot_volcano.Rd
man/prot.read_data.Rd
man/prot.report.Rd
man/prot.test_diff.Rd
man/prot.workflow.Rd
man/prot_to_map.Rd
man/read_file.Rd
man/read_flux.Rd
man/rna.filter_missing.Rd
man/rna.impute.Rd
man/rna.make_se.Rd
man/rna.plot_bar.Rd
man/rna.plot_corrheatmap.Rd
man/rna.plot_heatmap.Rd
man/rna.plot_imputation.Rd
man/rna.plot_numbers.Rd
man/rna.plot_pca.Rd
man/rna.plot_volcano.Rd
man/rna.read_data.Rd
man/rna.report.Rd
man/rna.workflow.Rd
man/svg_to_pdf.Rd
man/svg_to_png.Rd
man/theme_DEP1.Rd
man/theme_DEP2.Rd
pkgdown/extra.css
vignettes/references.bib
vignettes/vignette_proteomics.Rmd
vignettes/vignette_transcriptomics.Rmd
