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 21 Nov. 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
Downloads during the last 30 days
Get rewarded with contribution points by helping add
Reviews / comments / questions /suggestions ↴↴↴

Today's Hot Picks in Authors and Packages

crossrun  
Joint Distribution of Number of Crossings and Longest Run
Joint distribution of number of crossings and the longest run in a series of independent Bernoulli ...
Download / Learn more Package Citations See dependency  
deductive  
Data Correction and Imputation Using Deductive Methods
Attempt to repair inconsistencies and missing values in data records by using information from vali ...
Download / Learn more Package Citations See dependency  
SCBiclust  
Identifies Mean, Variance, and Hierarchically Clustered Biclusters
Identifies a bicluster, a submatrix of the data such that the features and observations within the s ...
Download / Learn more Package Citations See dependency  
r2resize  
In-Text Resize for Images, Tables and Fancy Resize Containers in 'shiny', 'rmarkdown' and 'quarto' Documents
Automatic resizing toolbar for containers, images and tables. Various resizable or expandable contai ...
Download / Learn more Package Citations See dependency  
RcppHNSW  
'Rcpp' Bindings for 'hnswlib', a Library for Approximate Nearest Neighbors
'Hnswlib' is a C++ library for Approximate Nearest Neighbors. This package provides a minimal R int ...
Download / Learn more Package Citations See dependency  
pkgdepends  
Package Dependency Resolution and Downloads
Find recursive dependencies of 'R' packages from various sources. Solve the dependencies to obtain ...
Download / Learn more Package Citations See dependency  

23,229

R Packages

199,929

Dependencies

62,984

Author Associations

23,230

Publication Badges

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