Other packages > Find by keyword >

pathwayTMB  

Pathway Based Tumor Mutational Burden
View on CRAN: Click here


Download and install pathwayTMB package within the R console
Install from CRAN:
install.packages("pathwayTMB")

Install from Github:
library("remotes")
install_github("cran/pathwayTMB")

Install by package version:
library("remotes")
install_version("pathwayTMB", "0.1.3")



Attach the package and use:
library("pathwayTMB")
Maintained by
Junwei Han
[Scholar Profile | Author Map]
All associated links for this package
First Published: 2021-07-15
Latest Update: 2022-08-09
Description:
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.
How to cite:
Junwei Han (2021). pathwayTMB: Pathway Based Tumor Mutational Burden. R package version 0.1.3, https://cran.r-project.org/web/packages/pathwayTMB. Accessed 04 Jun. 2026.
Previous versions and publish date:
0.1.0 (2021-07-15 09:50), 0.1.1 (2021-10-10 13:10), 0.1.2 (2022-05-18 10:30), 0.1.3 (2022-08-09 15:50)
Other packages that cited pathwayTMB R package
View pathwayTMB citation profile
Other R packages that pathwayTMB depends, imports, suggests or enhances
Complete documentation for pathwayTMB
Functions, R codes and Examples using the pathwayTMB R package
Some associated functions: GenePathwayOncoplots . PTMB_matrix . final_character . gene_path . genesmbol . get_PTMB . get_final_signature . get_mut_matrix . mut_matrix . plotKMcurves . plotMutInteract . plotROC . sur . 
Some associated R codes: data.R . main.R . visualization.R .  Full pathwayTMB package functions and examples
Downloads during the last 30 days

Today's Hot Picks in Authors and Packages

phers  
Calculate Phenotype Risk Scores
Use phenotype risk scores based on linked clinical and genetic data to study Mendelian disease and ...
Download / Learn more Package Citations See dependency  
murphydiagram  
Murphy Diagrams for Forecast Comparisons
Data and code for the paper by Ehm, Gneiting, Jordan and Krueger ('Of Quantiles and Expectiles: Con ...
Download / Learn more Package Citations See dependency  
nextGenShinyApps  
Craft Exceptional 'R Shiny' Applications and Dashboards with Novel Responsive Tools
Nove responsive tools for designing and developing 'Shiny' dashboards and applications. The scripts ...
Download / Learn more Package Citations See dependency  
AMPLE  
Shiny Apps to Support Capacity Building on Harvest Control Rules
Three Shiny apps are provided that introduce Harvest Control Rules (HCR) for fisheries management. ...
Download / Learn more Package Citations See dependency  
shinybusy  
Busy Indicators and Notifications for 'Shiny' Applications
Add indicators (spinner, progress bar, gif) in your 'shiny' applications to show the user that the ...
Download / Learn more Package Citations See dependency  
golem  
A Framework for Robust Shiny Applications
An opinionated framework for building a production-ready 'Shiny' application. This package contains ...
Download / Learn more Package Citations See dependency  

27,268

R Packages

233,548

Dependencies

72,590

Author Associations

27,205

Publication Badges

© Copyright since 2022. All right reserved, rpkg.net.  Based in Cambridge, Massachusetts, USA