Package: TraianProt 0.99.16

Samuel de la Camara Fuentes

TraianProt: TraianProt: a user-friendly R package for wide format proteomics data downstream analysis

A proteomics data analysis platform that enables the analysis of both label-free and labeled data from Data-Dependent or Data-Independent Acquisition mass spectrometry mode, supporting MaxQuant, MSFragger, DIA-NN, ProteoScape, and Proteome Discoverer output formats. TraianProt provides a comprehensive suite of stepwise downstream analysis modules, which includes data filtering, normalization procedures, and missing value imputation strategies. The platform also incorporates robust statistical frameworks for differential expression testing, with peptide-spectrum match level correction, thereby enhancing the reliability of biological interpretations.

Authors:Samuel de la Camara Fuentes [aut, cre]

TraianProt_0.99.16.tar.gz
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manual.pdf |manual.html✨
DESCRIPTION |NEWS
card.svg |card.png
TraianProt/json (API)

# Install 'TraianProt' in R:

install.packages('TraianProt', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/samueldelacamarafuentes/traianprot/issues

On BioConductor:TraianProt-0.99.16(bioc 3.24)

software proteomics massspectrometry dataimport normalization differentialexpression go dia-nn mass-spectrometry maxquant msfragger proteome-discoverer proteomics-data-analysis

5.48 score 3 stars 38 exports 247 dependencies

Last updated from:ee5dcc08bc. Checks:1 WARNING, 7 NOTE, 2 OK. Indexed: yes.

Target	Result	Time
bioc-checks	WARNING	262
linux-devel-x86_64	NOTE	508
source / vignettes	OK	430
linux-release-x86_64	NOTE	448
macos-release-arm64	NOTE	236
macos-oldrel-arm64	NOTE	277
windows-devel	NOTE	390
windows-release	NOTE	369
windows-oldrel	NOTE	359
wasm-release	OK	314

Exports:barplot_func boxplot_function collapse_technical_replicates corrplot_function Diferential_boxplot dotplot_func filter_valids gostplot_func Goterms_finder histogram identify_proteins igraph_analysis impute_data impute_KNN_data interactions_down interactions_up median_centering my_heatmap my_heatmap_differential normalization_func obtain_LOG.names obtain_unique_proteins pca plotCV2 postimputation_state preimputation_state qqplot_function quick_filtering runTraianProt scatterplot_function statistical_analysis traian_to_SE traianprot_power_curve tsne unique_peptides_filter venn_diagram volcano_plot volcano_plot_tiff

Dependencies:abind aisdk AnnotationDbi ape aplot askpass backports base64enc bbotk Biobase BiocBaseUtils BiocGenerics Biostrings bit bit64 bitops blob boot broom bslib cachem callr car carData caTools cellranger checkmate chron class cli cluster clusterProfiler codetools colorspace colourpicker commonmark cowplot cpp11 crayon crosstalk curl data.table DBI DelayedArray DEoptimR DEqMS Deriv digest doBy DOSE dplyr DT e1071 enrichit enrichplot evaluate farver fastmap fontawesome fontBitstreamVera fontLiberation fontquiver forecast formatR Formula fracdiff fs futile.logger futile.options future future.apply gdtools generics GenomicRanges ggExtra ggforce ggfun ggiraph ggnewscale ggplot2 ggplotify ggrepel ggtangle ggtree globals glue GO.db GOSemSim gplots gprofiler2 gridExtra gridGraphics gson gsubfn gtable gtools hash highr hms htmltools htmlwidgets httpuv httr httr2 igraph IRanges isoband jquerylib jsonlite KEGGREST KernSmooth knitr labeling laeken lambda.r later lattice lazyeval lgr lifecycle limma listenv lme4 lmtest magrittr MASS Matrix MatrixGenerics MatrixModels matrixStats memoise mgcv mime miniUI minqa mirai mlbench mlr3 mlr3learners mlr3measures mlr3misc mlr3pipelines mlr3tuning modelr moocore nanonext nlme nloptr nnet numDeriv openssl otel palmerpenguins paradox parallelly patchwork pbkrtest pheatmap pillar pkgconfig plotly plotrix plyr png polyclip prettyunits processx progress promises proto proxy PRROC ps purrr quantreg qvalue R6 ranger rappdirs rbibutils RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl Rdpack readxl reformulas rematch reshape2 rlang rmarkdown robustbase RSQLite Rtsne S4Arrays S4Vectors S7 sass scales scatterpie Seqinfo shiny shinydashboard shinyjs shinyWidgets sourcetools sp SparseArray SparseM sqldf statmod STRINGdb stringi stringr SummarizedExperiment survival sys systemfonts tibble tidydr tidyr tidyselect tidytree timeDate tinytex treeio tweenr urca utf8 uuid vcd vctrs VennDiagram VIM viridisLite withr writexl wrMisc wrProteo xfun xgboost xtable XVector yaml yulab.utils zoo

TraianProt: A Comprehensive package for Proteomics Data Analysis

Rendered fromTraianProt.Rmdusingknitr::rmarkdown

Last update: 2026-07-16
Started: 2026-04-27

Help page	Topics
Create Bar Plot from Enrichment Results	barplot_func
Create Boxplot of Sample Intensities	boxplot_function
Collapse Technical Replicates in Proteomics Data	collapse_technical_replicates
Correlation Matrix	corrplot_function
Differential Protein Boxplot	Diferential_boxplot
Create Dot Plot from Enrichment Results	dotplot_func
Filter proteins by valid values	filter_valids
Manhattan Plot for Functional Enrichment	gostplot_func
Find GO Terms (gprofiler2)	Goterms_finder
Plot a Histogram	histogram
Identify Proteins	identify_proteins
Perform igraph Analysis on STRING Subnetworks	igraph_analysis
Impute Missing Values using Down-Shifted Normal Distribution	impute_data
Impute missing data using k-NN	impute_KNN_data
Plot STRING Interactions for Down-regulated Proteins	interactions_down
Get STRING Interactions for Up-regulated Proteins	interactions_up
Perform median centering normalization	median_centering
Base R Heatmap	my_heatmap
Differential Protein Heatmap (ggplot)	my_heatmap_differential
Apply Normalization to LOG2 Columns	normalization_func
Obtain LOG2 Column Names	obtain_LOG.names
Obtain Unique Proteins Between Conditions	obtain_unique_proteins
Custom PCA Plot (Base R)	pca
Plot Coefficient of Variation vs. Mean	plotCV2
Plot Post-Imputation Density	postimputation_state
Plot Missingness Pattern	preimputation_state
Create a Q-Q Plot	qqplot_function
Quick Data Filtering	quick_filtering
Launch the TraianProt Shiny Application	runTraianProt
Create a Scatterplot with Marginal Densities	scatterplot_function
Limma function for statistical analysis	statistical_analysis
Export TraianProt results to SummarizedExperiment	traian_to_SE
Create power curve	traianprot_power_curve
t-SNE Plot	tsne
Filter Proteins by Unique Peptide Counts	unique_peptides_filter
Create a Venn Diagram	venn_diagram
This function generates an interactive volcano plot using the 'plotly' package based on differential expression results.	volcano_plot
Create a Static Volcano Plot for Publication	volcano_plot_tiff

Package: TraianProt 0.99.16

TraianProt: TraianProt: a user-friendly R package for wide format proteomics data downstream analysis

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