ICBioMark

0.1.4

Data-Driven Design of Targeted Gene Panels for Estimating Immunotherapy Biomarkers

0packages depend

3Kdownloads / year

46.7%test coverage

0/13checks pass

Overview

About

Maintained by Jacob R. BradleyFirst published 2021-02-174 releasesCRAN page ↗

Implementation of the methodology proposed in 'Data-driven design of targeted gene panels for estimating immunotherapy biomarkers', Bradley and Cannings (2021) arXiv:2102.04296. 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.

Install

R (CRAN)Ubuntu (r2u)openSUSE (OBS)

install.packages("ICBioMark", repos = "https://cloud.r-project.org/")

Installs the current CRAN release. Prebuilt binaries on Windows and macOS.

Release

# enable cranapt (r2u) if it is not already set up, then install
grep -rqs r2u.stat.illinois.edu /etc/apt/sources.list /etc/apt/sources.list.d/ \
  || curl -fsSL https://raw.githubusercontent.com/eddelbuettel/r2u/master/inst/scripts/add_cranapt_noble.sh | sudo bash
sudo apt install -y r-cran-icbiomark

Fast Ubuntu binaries via r2u (no compilation). The cranapt setup runs once and is skipped when it is already enabled.

bspm (used by r2u) also needs make: sudo apt install make

# add the autoCRAN OBS repo (Tumbleweed) if it is missing, then install
zypper -q lr | grep -qi autoCRAN \
  || sudo zypper addrepo https://download.opensuse.org/repositories/devel:/languages:/R:/autoCRAN/openSUSE_Tumbleweed/devel:languages:R:autoCRAN.repo
sudo zypper install -y R-ICBioMark

RPMs auto-built from CRAN on openSUSE OBS (Tumbleweed).

Health

CRAN checks

13NOTE

Failing flavors

NOTE r-devel-linux-x86_64-debian-clang
NOTE r-devel-linux-x86_64-debian-gcc
NOTE r-devel-linux-x86_64-fedora-clang
NOTE r-devel-linux-x86_64-fedora-gcc
NOTE r-devel-windows-x86_64
NOTE r-oldrel-macos-arm64
NOTE r-oldrel-macos-x86_64
NOTE r-oldrel-windows-x86_64
NOTE r-patched-linux-x86_64
NOTE r-release-linux-x86_64
NOTE r-release-macos-arm64
NOTE r-release-macos-x86_64
NOTE r-release-windows-x86_64

Slowest check: 1.9 min · r-oldrel-windows-x86_64

Check history

NOTE2026-03-10
0 OK · 14 NOTE · 0 WARNING · 0 ERROR · 0 FAILURE

Documentation

Documentation signals are not tracked yet for this package.

Downloads

CRAN downloads in the past year

Rank #13,312 · ~8/day · ~250/mo

ICBioMark Releases R versions

Daily download trend is not available in this view yet.

28630 days

79090 days

3K1 year

Compare downloads with other packages →

Also on162 r2u32 autocran24 c2d4u

Dependencies

Declared dependencies

9 external dependencies (excludes base and recommended)

Depends (1)

R >= 2.10

Imports (11)

statsutilsglmnetMatrixdplyr purrr latex2exp matrixStats ggplot2 gglasso PRROC

LinkingTo (0)

none

Suggests (1)

testthat

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

0indirect

Nothing depends on this yet.

Code & Tests

Datasets

People & History

People (2)

Maintainer (1)

Jacob R. Bradley

Author, Maintainer

Authors (2)

Jacob R. Bradley

Author, Maintainer

Timothy I. Cannings

Author

Package Timeline

4 releases. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
R
R 4.5.0 released · 2025-04-11
R
R 4.4.0 released · 2024-04-24
R
R 4.3.0 released · 2023-04-21
R
R 4.2.0 released · 2022-04-22
0.1.4Latest
2021-11-15 · current release · diff ↗
R
R 4.1.0 released · 2021-05-18
0.1.2
2021-03-18 · diff ↗
0.1.1
2021-03-05 · diff ↗
unarchivedReturned to CRAN
2021-03-05
archivedRemoved from CRAN
2021-03-04
policy violation On Internet access
0.1.0
2021-02-17
R
R 4.0.0 released · 2020-04-24

Package metadata

First published: 2021-02-17
Total releases: 4 / 5 yrs
License: MIT + file LICENSE OSI
Download size: 3.0 MB
Installed size: not tracked yet
With dependencies: not tracked yet

Appears in task views

Genomics, Proteomics, Metabolomics, Transcriptomics, and Other Omics

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