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]
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 09 May. 2025.
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)
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
04/0904/1004/1104/1204/1304/1404/1504/1604/1704/1804/1904/2004/2104/2204/2304/2404/2504/2604/2704/2804/2904/3005/0105/0205/0305/0405/0505/0605/0705/08Downloads for pathwayTMB246810121416182022242628TrendBars

Today's Hot Picks in Authors and Packages

assertive.numbers  
Assertions to Check Properties of Numbers
A set of predicates and assertions for checking the properties of numbers. This is mainly for use ...
Download / Learn more Package Citations See dependency  
disparityfilter  
Disparity Filter Algorithm for Weighted Networks
The disparity filter algorithm is a network reduction technique to identify the 'backbone' structur ...
Download / Learn more Package Citations See dependency  
SACOBRA  
Self-Adjusting COBRA
Performs surrogate-assisted optimization for expensive black-box constrained problems. ...
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  

24,205

R Packages

207,311

Dependencies

65,312

Author Associations

24,206

Publication Badges

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