mastR

Markers Automated Screening Tool in R

Bioconductor version: Release (3.17)

mastR is an R package designed for automated screening of signatures of interest for specific research questions. The package is developed for generating refined lists of signature genes from multiple group comparisons based on the results from edgeR and limma differential expression (DE) analysis workflow. It also takes into account the background noise of tissue-specificity, which is often ignored by other marker generation tools. This package is particularly useful for the identification of group markers in various biological and medical applications, including cancer research and developmental biology.

Author: Jinjin Chen [aut, cre] , Ahmed Mohamed [aut, ctb] , Chin Wee Tan [ctb]

Maintainer: Jinjin Chen <chen.j at wehi.edu.au>

Citation (from within R, enter citation("mastR")):

Installation

To install this package, start R (version "4.3") and enter:

if (!require("BiocManager", quietly = TRUE))
    install.packages("BiocManager")

BiocManager::install("mastR")

For older versions of R, please refer to the appropriate Bioconductor release.

Documentation

To view documentation for the version of this package installed in your system, start R and enter:

browseVignettes("mastR")

mastR_Demo	HTML	R Script
Reference Manual	PDF
NEWS	Text
LICENSE	Text

Details

biocViews	DifferentialExpression, GeneExpression, Software, Transcriptomics, Visualization
Version	1.0.0
In Bioconductor since	BioC 3.17 (R-4.3) (< 6 months)
License	MIT + file LICENSE
Depends	R (>= 4.3.0)
Imports	AnnotationDbi, Biobase, dplyr, edgeR, ggplot2, ggpubr, graphics, grDevices, GSEABase, limma, Matrix, methods, msigdb, org.Hs.eg.db, patchwork, SeuratObject, SingleCellExperiment, stats, SummarizedExperiment, tidyr, utils
Linking To
Suggests	BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR
System Requirements
Enhances
URL	https://davislaboratory.github.io/mastR
Bug Reports	https://github.com/DavisLaboratory/mastR/issues

Depends On Me
Imports Me
Suggests Me
Links To Me
Build Report

Package Archives

Follow Installation instructions to use this package in your R session.

Source Package	mastR_1.0.0.tar.gz
Windows Binary	mastR_1.0.0.zip (64-bit only)
macOS Binary (x86_64)	mastR_1.0.0.tgz
macOS Binary (arm64)	mastR_1.0.0.tgz
Source Repository	git clone https://git.bioconductor.org/packages/mastR
Source Repository (Developer Access)	git clone git@git.bioconductor.org:packages/mastR
Bioc Package Browser	https://code.bioconductor.org/browse/mastR/
Package Short Url	https://bioconductor.org/packages/mastR/
Package Downloads Report	Download Stats