CaMutQC
An R package for mutation quality control of cancer genomic sequening dataset
Science Score: 39.0%
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Low similarity (15.4%) to scientific vocabulary
Keywords
Repository
An R package for mutation quality control of cancer genomic sequening dataset
Basic Info
- Host: GitHub
- Owner: likelet
- License: gpl-3.0
- Language: R
- Default Branch: master
- Homepage: https://seqworld.com/CaMutQC/
- Size: 70.6 MB
Statistics
- Stars: 7
- Watchers: 2
- Forks: 0
- Open Issues: 0
- Releases: 10
Topics
Metadata Files
README.md
Integrative quality control of cancer somatic mutations with
Cancer Mutation Quality Control
Introduction
The quality control of cancer somatic mutations has a great significance in the research of cancer genomics. It helps reduce the noise, systematic bias, as well as the false positive rate in dataset, and to pick out candidate mutations related to tumorigenesis. However, existing tools were not designed especially for cancer somatic mutations, and parameters and filtering standards used are different among them. Besides, there is no such a platform, database or tool stores or summarizes the standards for filtration of cancer somatic mutations applied in previous studies, which increases the time and energy spent on related research.
Therefore, we present this R package, CaMutQC, for the comprehensive filtration and selection of cancer somatic mutations for tumor-normal paired samples. CaMutQC is able to filter false positive mutations generated due to technical issues, as well as to select candidate cancer mutations through a series of well-structured functions by labeling mutations with various flags.
Also, a detailed and vivid filter report will be generated after completing a whole filtration or selection section.
Installation
Through Bioconductor (recommended) to get the most stable version: ```R if (!require("BiocManager", quietly = TRUE)) install.packages("BiocManager")
the latest version is on the devel branch, but might not be the most stable version
BiocManager::install(version='devel')
the most stable version is on the release branch (by default)
BiocManager::install("CaMutQC") ```
Through Github to get the latest version: ```R
install the latest version from GitHub
if(!require(devtools)) install.packages("devtools") devtools::install_github("likelet/CaMutQC") ```
Usage
This is a simple workflow of CaMutQC.
A detailed manual can be found here.
Shiny APP
We developed a Shiny application for CaMutQC to enhance its accessibility. Users can use the following code to launch Shiny app build with the package. ```R pkgrequiredshiny <- c('shiny','shinyjs', 'shinyFiles', 'DT')
Install required packages
checkPackage <- function(pkg){ if (!requireNamespace(pkg, quietly = TRUE)) { stop(paste0("Package ", pkg, " needed for shiny app. Please install it."), call. = FALSE) } } invisible(lapply(pkgrequiredshiny, checkPackage))
run shiny app from shiny package
shiny::runApp(system.file("shiny", package = "CaMutQC")) ```
Author
This software was mainly developed by:
- Xin Wang, sylviawang555@gmail.com
Supervised by
- Jian Ren from School of Life Sciences in Sun Yat-sen University
- Qi Zhao from Bioinformatic Center of Sun Yat-sen University Cancer Center
Maintainer
Citation
Xin Wang, Tengjia Jiang, Ao Shen, Yaru Chen, Yanqing Zhou, Jie Liu, Shuhan Zhao, Shifu Chen, Jian Ren, and Qi Zhao. CaMutQC: An R package for integrative quality control and filtration of cancer somatic mutations. Computational and Structural Biotechnology Journal. 2025;27:3147–3154. https://doi.org/10.1016/j.csbj.2025.07.011
Owner
- Name: Qi ZHAO
- Login: likelet
- Kind: user
- Location: China,Guangzhou
- Company: Sun Yat-sen University Cancer center
- Website: http://seqworld.com/
- Repositories: 12
- Profile: https://github.com/likelet
Associate Professor, Cancer genomics @ Sun Yat-sen University Cancer Center.
GitHub Events
Total
- Push event: 13
- Gollum event: 2
- Create event: 1
Last Year
- Push event: 13
- Gollum event: 2
- Create event: 1
Issues and Pull Requests
Last synced: 10 months ago
All Time
- Total issues: 1
- Total pull requests: 38
- Average time to close issues: 17 days
- Average time to close pull requests: about 9 hours
- Total issue authors: 1
- Total pull request authors: 3
- Average comments per issue: 6.0
- Average comments per pull request: 0.0
- Merged pull requests: 38
- Bot issues: 0
- Bot pull requests: 0
Past Year
- Issues: 0
- Pull requests: 0
- Average time to close issues: N/A
- Average time to close pull requests: N/A
- Issue authors: 0
- Pull request authors: 0
- Average comments per issue: 0
- Average comments per pull request: 0
- Merged pull requests: 0
- Bot issues: 0
- Bot pull requests: 0
Top Authors
Issue Authors
- shawez (1)
Pull Request Authors
- Wangxin555 (39)
- LiuJie1117 (1)
- ShuhanZhao (1)
Top Labels
Issue Labels
Pull Request Labels
Packages
- Total packages: 1
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Total downloads:
- bioconductor 3,915 total
- Total dependent packages: 0
- Total dependent repositories: 0
- Total versions: 6
- Total maintainers: 1
bioconductor.org: CaMutQC
An R Package for Comprehensive Filtration and Selection of Cancer Somatic Mutations
- Homepage: https://github.com/likelet/CaMutQC
- Documentation: https://bioconductor.org/packages/release/bioc/vignettes/CaMutQC/inst/doc/CaMutQC.pdf
- License: GPL-3
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Latest release: 1.4.5
published 10 months ago
Rankings
Maintainers (1)
Dependencies
- DT * imports
- clusterProfiler * imports
- dplyr * imports
- ggplot2 * imports
- org.Hs.eg.db * imports
- stringr * imports
- vcfR * imports
- knitr * suggests
- rmarkdown * suggests