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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 22 Dec. 2024.
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
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