This package was removed from CRAN on 2025-09-20. Its history is shown below.

Reason: errors were not corrected in time

Details below reflect version 0.1.3, its last release before removal.

pathwayTMB

0.1.3

Pathway Based Tumor Mutational Burden

0packages depend

–downloads / year

–test coverage

–checks pass

Overview

About

Maintained by Junwei Han4 releasesCRAN page ↗

A systematic bioinformatics tool to develop a new pathway-based gene panel for tumor mutational burden (TMB) assessment (pathway-based tumor mutational burden, PTMB), using somatic mutations files in an efficient manner from either The Cancer Genome Atlas sources or any in-house studies as long as the data is in mutation annotation file (MAF) format. Besides, we develop a multiple machine learning method using the sample's PTMB profiles to identify cancer-specific dysfunction pathways, which can be a biomarker of prognostic and predictive for cancer immunotherapy.

Install

R (source archive)Ubuntu (r2u)

url <- "https://cran.r-project.org/src/contrib/Archive/pathwayTMB/pathwayTMB_0.1.3.tar.gz"
pkgFile <- "pathwayTMB_0.1.3.tar.gz"
download.file(url, pkgFile)
install.packages(pkgFile, type = "source", repos = NULL)

This package is no longer on CRAN, so install.packages() cannot fetch it by name. This downloads the last archived source (0.1.3) and builds it locally. Install its dependencies first, and note that building from source needs the usual compiler toolchain.

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-pathwaytmb

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

Health

CRAN checks

CRAN check results are not tracked yet.

Code health

Yes

Tests · ratio 0.00

not tracked

Coverage

100%

Documentation · exports

Dependencies · direct

Documentation

READMENoVignettesYes · dynamicpkgdown siteNoNEWSNoCode of conductNoContributing guideNo

Examples that run: 100%
Documented parameters: 100%
Return-value docs: 100%
References docs: 0%

Downloads

Releases R versions

Daily download trend is not available in this view yet.

Compare downloads with other packages →

Also on86 r2u427 bioconda

Dependencies

Declared dependencies

21 external dependencies (excludes base and recommended)

Depends (1)

R >= 4.1.0

Imports (16)

BiocGenerics purrrutilsglmnet randomForeststatssurvivalsurvminer caret data.table RColorBrewergrDevicespROCgraphicsmaftools clusterProfiler

LinkingTo (0)

none

Suggests (10)

stringi knitr rmarkdown testthat BiocManager xfun e1071 qpdf tinytex spelling

Enhances (0)

none

Dependency license breakdown →

Reverse dependencies

0direct

–indirect (not tracked)

Nothing depends on this yet.

Code & Tests

Code Composition

R 773 (50%)Rd 554 (36%)Vignettes 167 (11%)CSS 37 (2%)

Code characteristics

Cyclomatic complexity: 5.0 median / 23 max

Test coverage

Line coverage

–

Expression

–

Tests / Examples

–

Functions

7 7 exported

Complexity

7.1 avg / 23 max

Call network

7 nodes / 0 edges

Test coverage has not been measured for this package yet; nodes fall back to a neutral fill.

Call graph

Open call graph →

Loading call graph…

Lowest coverage

Per-function coverage is not measured for this package yet.

Datasets

Bundled datasets · 3

Name	Class	Rows × Cols	Also ships in
PTMB_matrix	data.frame	27 × 35	–
final_character	vector	–	–
sur	data.frame	110 × 2	–

People & History

People (2)

Maintainer (1)

Junwei Han

Author, Maintainer, Copyright holder

Authors (2)

Junwei Han

Author, Maintainer, Copyright holder

Xiangmei Li

Author

Junwei Han

Author, Maintainer, Copyright holder

Package Timeline

4 releases. Pick two to compare their code metrics. R releases are shown for context.

R
R 4.6.0 released · 2026-04-24
archivedRemoved from CRAN
2025-09-20
errors were not corrected in time
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
0.1.3
2022-08-09 · diff ↗
0.1.2
2022-05-18 · diff ↗
unarchivedReturned to CRAN
2022-05-18
archivedRemoved from CRAN
2022-05-07
calls defunct 'default.stringsAsFactors()'
R
R 4.2.0 released · 2022-04-22
0.1.1
2021-10-10 · diff ↗
0.1.0
2021-07-15
R
R 4.1.0 released · 2021-05-18

Package metadata

Total releases: 4
License: GPL (>= 2) OSI
Minimum R: ≥ 4.1.0
Bundled data: 184 KB / 6 files
Download size: not tracked yet
Installed size: not tracked yet
With dependencies: not tracked yet

Report a problem with this page →