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The combiroc package is a totally new music in multi-markers analysis: an R package for efficient and easy combinatorial selection of biomarkers and sensitivity/specificity-driven prioritization of features.

Latest version introduces new features to workon single-cell RNAseq datasets too, selecting smaller markers sub-signatures that can be used to efficiently identify and annotate cell clusters.

This is the development version of CombiROC package (combiroc), code in this repo is work in progress and it is uploaded here "as-is" with no warranties implied. Improvements and new features will be added on a regular basis, please check on this github page for new features and releases.

The CombiROC approach was first released as a Shiny Application which is still available atcombiroc.eu but it has limited features as well as low computational power and isnot further maintained. If you need to cite the web-app please refer toMazzara et al. Scientific Reports 2017 andBombaci & Rossi, Methods Mol Biol 2019.

For full capabilities and customized analyseswe suggest to use the R package and not the Shiny app version. You can install the combiroc package fromCRAN or the latest development version from this repo (see below).

If you are using the combirocpackage in your research, please cite our"Less is more" bioRxiv preprint:Ferrari et al.Combiroc: when 'less is more' in bulk and single cell marker signatures. bioRxiv 2022.01.17.476603; doi: https://doi.org/10.1101/2022.01.17.476603

ThebioRxiv preprint's Supplementary Material 1 and 2 can be accessed here:

• Supplementary Material 1 (Standard vignette):Standard worlkflow.
• Supplementary Material 2 (Additional vignette):scRNAseq workflow.

Be aware that CRAN version is not necessarily in sync with the development version:current version on CRAN is v.0.3.4.
Documentation on these pages refers to the latest development version and can quickly evolve: if you install combiroc from CRAN please be sure to refer to documentation available on CRAN's combiroc page.

# You can install combiroc pulling it from CRAN:install.packages("combiroc")

# To install the most recent development version from this repository install "remotes" first:install.packages("remotes")library(remotes)# remotes is a lightweight replacement of install functions from devtools# if you already have devtools, you can also use devtools::install_github()# Then install the development version of CombiROC:remotes::install_github("ingmbioinfo/combiroc",dependencies=TRUE,build_vignettes=TRUE)

Full documentation is in the package's vignette. You can also find the rendered version of the vignette in thecombiroc-package website created withpkgdown.

library(combiroc)# load the preformatted demo dataset# (you can load a dataset of yours using load_data() function: see full docs)data<-demo_data# shape it in long format (prone to plotting)data_long<- combiroc_long(data)# study the distribution of you markers' signal# arguments values to be adjusted according to  datadistr<- markers_distribution(data_long,case_class='A',y_lim=0.0015,x_lim=3000,signalthr_prediction=TRUE,min_SE=40,min_SP=80,boxplot_lim=2000)# explore the distr object: boxplot of signalsdistr$Boxplot# explore the distr object: densities of classes with signal threshold (signalthr)distr$Density_plotdistr$Density_summary# explore the distr object: ROC and its coordinatesdistr$ROChead(distr$Coord,n=10)# combinatorial analysis, indicatinf case class anf for combinations of up to 3 markers:tab<- combi(data,signalthr=328,combithr=1,case_class="A",max_length=3)# ranked combinationsrmks<- ranked_combs(tab,min_SE=40,min_SP=80)# check ranked combinationsrmks$tablermks$bubble_chart# results report for specific markers/combinationsreports<-roc_reports(data,markers_table=tab,case_class='A',single_markers=c('Marker1'),selected_combinations= c(11,15))# results outputsreports$Plotreports$Metrics

If you find a bug, or to share ideas for improvement, feel free tostart an issue. We do have a roadmap but we also listen!

• Package authors and maintainers: Ivan Ferrari & Riccardo L. Rossi
• Original code of Shiny App: Saveria Mazzara
• Initial idea & conception: Mauro Bombaci

We were so happy to finally had the chance to develop the combiroc package that we felt very "rock": this is why the combiroc hexagon sticker logo is a homage toEddie Van Halen who left us in 2020, and the "Frankenstrat", hisiconic guitar.