Files in vladpetyuk/vp.misc
Miscellaneous functions used by Vlad Petyuk for proteomics data analysis
.Rbuildignore
.gitignore
DESCRIPTION
NAMESPACE
R/colorschemes.R
R/concatenate_by_features.R
R/custom_dist.R
R/data.R
R/eset_lm_1.R
R/exhaustive_ratios.R
R/handling_PTMs.R
R/heatmap.3.R
R/heatmap.plus.2.R
R/image_msnset.R
R/knn_imputation.r
R/limma_a_b.R
R/list_objects.R
R/lr_modeling.R
R/lr_modeling_old.R
R/make.unique.2.R
R/mixed_effects_anova.R
R/msnset2txt.R
R/norm_by_global.R
R/norm_by_ref.R
R/normalize_by_feature_property.R
R/plotAUC.R
R/plot_annHeatmap2.R
R/plot_feature.R
R/plot_pca.R
R/plot_umap.R
R/presense_absense.R
R/protein_inference.R
R/readMaxQuantPeptides.R
R/readMaxQuantProtGroups.R
R/readMaxQuantSummary.R
R/read_SkyLine.R
R/remove_covariate.R
R/rf_modeling.R
R/rollup.R
R/subset_by_size_enrichments.R
R/volcano_plot.R
R/xtable2.R
README.md
TODO.md
data/cptac_oca.RData
data/longitudinal_biomarker_study.RData
data/phospho_identifications_rat.RData
data/srm_msnset.RData
inst/extdata/FASTAs/rattus_norvegics_uniprot_2018_09.fasta.gz
inst/extdata/MaxQuant/proteinGroups.txt.xz
inst/extdata/MaxQuant/summary.txt
inst/extdata/MaxQuantPep/peptides.txt.gz
inst/extdata/MaxQuantPep/summary.txt.gz
inst/extdata/MaxQuant_O18/proteinGroups.txt.xz
inst/extdata/MaxQuant_O18/summary.txt
inst/extdata/titin_peptide_mapping/titin.fasta.gz
inst/extdata/titin_peptide_mapping/titin_peptides.txt.gz
man/colorschemes.Rd
man/concatenate_by_features.Rd
man/dist.Rd
man/eset_lm.Rd
man/eset_presence_absence.Rd
man/exhaustive_ratios.Rd
man/heatmap.3.Rd
man/heatmap.plus.2.Rd
man/image_msnset.Rd
man/keep_longest_isoform_per_gene.Rd
man/knn_imputation.Rd
man/limma_a_b.Rd
man/longitudinal_biomarker_study.Rd
man/lr_modeling.Rd
man/make.unique.2.Rd
man/map_PTM_sites.Rd
man/mixed_effects_anova.Rd
man/msnset.Rd
man/msnset2txt.Rd
man/normalizeByGlob.Rd
man/normalizeByRef.Rd
man/normalize_by_feature_property.Rd
man/oca.set.Rd
man/plotAUC.Rd
man/plot_annHeatmap2.Rd
man/plot_feature.Rd
man/plot_pca_v1.Rd
man/plot_umap.Rd
man/protein_inference.Rd
man/readMaxQuantPeptides.Rd
man/readMaxQuantProtGroups.Rd
man/readMaxQuantSummary.Rd
man/readSkyLinePRR.Rd
man/remove_covariate.Rd
man/rf_modeling.Rd
man/rrollup.Rd
man/subset_by_size.Rd
man/volcano_plot.Rd
man/xtable2.Rd
sandbox/old_ML/lr_modeling.R
sandbox/old_ML/lr_modeling_old.R
sandbox/old_ML/rf_modeling.R
vignettes/fuzzy_cmeans.Rmd
vignettes/fuzzy_cmeans.html
vignettes/heatmap.plus.2.Rmd
vignettes/heatmap.plus.2.html
vignettes/heatmap_examples.Rmd
vignettes/heatmap_examples.html
vignettes/id_conversion.Rmd
vignettes/id_conversion.html
vignettes/ontology_overrepresentation.Rmd
vignettes/ontology_overrepresentation.html
vignettes/peptide_mapping_example_1.Rmd
vignettes/peptide_mapping_example_1.html
vignettes/wgcna_example.Rmd
vignettes/wgcna_example.html
