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ICBioMark
View on CRAN: Click
here
Download and install ICBioMark package within the R console
Install from CRAN:
install.packages("ICBioMark")
Install from Github:
library("remotes")
install_github("cran/ICBioMark") Install by package version:
library("remotes")
install_version("ICBioMark", "0.1.4") Attach the package and use:
library("ICBioMark")
Maintained by
Jacob R. Bradley
[Scholar Profile | Author Map]
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-02-17
Latest Update: 2021-11-15
Description:
Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) . This package allows the user to fit generative models of mutation from an annotated mutation dataset, and then further to produce tunable linear estimators of exome-wide biomarkers. It also contains functions to simulate mutation annotated format (MAF) data, as well as to analyse the output and performance of models.
How to cite:
Jacob R. Bradley (2021). ICBioMark: Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers. R package version 0.1.4, https://cran.r-project.org/web/packages/ICBioMark. Accessed 22 Sep. 2026.
Previous versions and publish date:
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Other R packages that ICBioMark depends,
imports, suggests or enhances
Complete documentation for ICBioMark
Functions, R codes and Examples using
the ICBioMark R package
Some associated functions: ICBioMark . ensembl_gene_lengths . example_first_pred_tmb . example_gen_model . example_maf_data . example_predictions . example_refit_panel . example_refit_range . example_tables . example_tib_tables . example_tmb_tables . fit_gen_model . fit_gen_model_uninteract . fit_gen_model_unisamp . generate_maf_data . get_K . get_auprc . get_biomarker_from_maf . get_biomarker_tables . get_gen_estimates . get_mutation_dictionary . get_mutation_tables . get_p . get_panels_from_fit . get_predictions . get_r_squared . get_stats . get_table_from_maf . nsclc_maf . nsclc_survival . pred_first_fit . pred_intervals . pred_refit_panel . pred_refit_range . vis_model_fit .
Some associated R codes: ICBioMark.R . ensembl_gene_lengths.R . example_data.R . gen_model.R . generate_maf_data.R . maf_to_tables.R . metrics.R . nsclc_data.R . predict.R . Full ICBioMark package functions and examples
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