CRAN/E | pathwayTMB

pathwayTMB

Pathway Based Tumor Mutational Burden

Installation

About

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.

Key Metrics

Version 0.1.3
R ≥ 4.1.0
Published 2022-08-09 795 days ago
Needs compilation? no
License GPL-2
License GPL-3
CRAN checks pathwayTMB results
Language en-US

Downloads

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Maintainer

Maintainer

Junwei Han

Authors

Junwei Han

aut / cre / cph

Xiangmei Li

aut

Material

Reference manual
Package source

Vignettes

pathwayTMB

macOS

r-release

arm64

r-oldrel

arm64

r-release

x86_64

r-oldrel

x86_64

Windows

r-devel

x86_64

r-release

x86_64

r-oldrel

x86_64

Old Sources

pathwayTMB archive

Depends

R ≥ 4.1.0

Imports

BiocGenerics
purrr
utils
glmnet
randomForest
stats
survival
survminer
caret
data.table
RColorBrewer
grDevices
pROC
graphics
maftools
clusterProfiler

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