Package: combiroc 0.3.4
Riccardo L. Rossi
combiroc: Selection and Ranking of Omics Biomarkers Combinations Made Easy
Provides functions and a workflow to easily and powerfully calculating specificity, sensitivity and ROC curves of biomarkers combinations. Allows to rank and select multi-markers signatures as well as to find the best performing sub-signatures, now also from single-cell RNA-seq datasets. The method used was first published as a Shiny app and described in Mazzara et al. (2017) <doi:10.1038/srep45477> and further described in Bombaci & Rossi (2019) <doi:10.1007/978-1-4939-9164-8_16>, and widely expanded as a package as presented in the bioRxiv pre print Ferrari et al. <doi:10.1101/2022.01.17.476603>.
Authors:
combiroc_0.3.4.tar.gz
combiroc_0.3.4.zip(r-4.5)combiroc_0.3.4.zip(r-4.4)combiroc_0.3.4.zip(r-4.3)
combiroc_0.3.4.tgz(r-4.4-any)combiroc_0.3.4.tgz(r-4.3-any)
combiroc_0.3.4.tar.gz(r-4.5-noble)combiroc_0.3.4.tar.gz(r-4.4-noble)
combiroc_0.3.4.tgz(r-4.4-emscripten)combiroc_0.3.4.tgz(r-4.3-emscripten)
combiroc.pdf |combiroc.html✨
combiroc/json (API)
NEWS
| # Install 'combiroc' in R: |
| install.packages('combiroc', repos = c('https://ingmbioinfo.r-universe.dev', 'https://cloud.r-project.org')) |
Bug tracker:https://github.com/ingmbioinfo/combiroc/issues
- demo_data - A demo dataset with proteomics markers
- demo_unclassified_data - A demo dataset with unlabeled proteomics markers
Last updated 3 months agofrom:ebb7c2eb38. Checks:ERROR: 1 WARNING: 6. Indexed: yes.
| Target | Result | Date |
|---|---|---|
| Doc / Vignettes | FAIL | Aug 28 2024 |
| R-4.5-win | WARNING | Aug 28 2024 |
| R-4.5-linux | WARNING | Aug 28 2024 |
| R-4.4-win | WARNING | Aug 28 2024 |
| R-4.4-mac | WARNING | Aug 28 2024 |
| R-4.3-win | WARNING | Aug 28 2024 |
| R-4.3-mac | WARNING | Aug 28 2024 |
Exports:combicombi_scorecombiroc_longcombs_withload_datamarkers_distributionranked_combsroc_reportsseurat_to_combirocshow_markerssingle_markers_statistics
Dependencies:clicolorspacecpp11dplyrfansifarvergenericsggplot2gluegtablegtoolsisobandlabelinglatticelifecyclemagrittrMASSMatrixmgcvmomentsmunsellnlmepillarpkgconfigplyrpROCpurrrR6RColorBrewerRcpprlangscalesstringistringrtibbletidyrtidyselectutf8vctrsviridisLitewithr
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Compute combinations. | combi |
| Compute the combi score using glm(link='binomial') models and optionally classifies the samples. | combi_score |
| Reshape combiroc data in long format. | combiroc_long |
| Show combinations with given markers. | combs_with |
| A demo dataset with proteomics markers | demo_data |
| A demo dataset with unlabeled proteomics markers | demo_unclassified_data |
| Load CombiROC data. | load_data |
| Show distribution of intensity values for all the markers both singularly and all together. | markers_distribution |
| Rank combinations. | ranked_combs |
| Train logistic regression and compute ROC. | roc_reports |
| Load CombiROC data. | seurat_to_combiroc |
| Show the composition of combinations. | show_markers |
| Provide statistics for each marker. | single_markers_statistics |
