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mastR

Markers Automated Screening Tool in R


Bioconductor version: Release (3.18)

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 1.2.3
In Bioconductor since BioC 3.17 (R-4.3) (1 year)
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
System Requirements
URL https://davislaboratory.github.io/mastR
Bug Reports https://github.com/DavisLaboratory/mastR/issues
See More
Suggests BiocManager, BiocStyle, BisqueRNA, clusterProfiler, ComplexHeatmap, depmap, enrichplot, ggrepel, ggvenn, gridExtra, jsonlite, knitr, rmarkdown, RobustRankAggreg, rvest, scuttle, singscore, splatter, testthat (>= 3.0.0), UpSetR
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Package Archives

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

Source Package mastR_1.2.3.tar.gz
Windows Binary mastR_1.2.3.zip
macOS Binary (x86_64) mastR_1.2.3.tgz
macOS Binary (arm64) mastR_1.2.3.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
Old Source Packages for BioC 3.18 Source Archive