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 26 Aug. 2026.
Previous versions and publish date:
(2026-07-09 06:39), 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

SelvarMix  
Regularization for Variable Selection in Model-Based Clustering and Discriminant Analysis
Performs a regularization approach to variable selection in themodel-based clustering and classifica ...
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  
RCytoGPS  
Using Cytogenetics Data in R
Defines classes and methods to process text-based cytogenetics using the CytoGPS web site, then imp ...
Download / Learn more Package Citations See dependency  
leafgl  
High-Performance 'WebGl' Rendering for Package 'leaflet'
Provides bindings to the 'Leaflet.glify' JavaScript library which extends the 'leaflet' JavaScript l ...
Download / Learn more Package Citations See dependency  
clinUtils  
General Utility Functions for Analysis of Clinical Data
Utility functions to facilitate the import, the reporting and analysis of clinical data. Example ...
Download / Learn more Package Citations See dependency  
PCADSC  
Tools for Principal Component Analysis-Based Data Structure Comparisons
A suite of non-parametric, visual tools for assessing differences in data structures for two datase ...
Download / Learn more Package Citations See dependency  

28,332

R Packages

239,283

Dependencies

75,113

Author Associations

28,333

Publication Badges

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