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Bioconductor - mastR

mastR

This is the released version of mastR; for the devel version, see mastR.

Markers Automated Screening Tool in R

Bioconductor version: Release (3.21)

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] ORCID: 0000-0001-7923-5723 , Ahmed Mohamed [aut, ctb] ORCID: 0000-0001-6507-5300 , Chin Wee Tan [ctb] ORCID: 0000-0001-9695-7218

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

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

To install this package, start R (version "4.5") 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")
Details biocViews DifferentialExpression, GeneExpression, Software, Transcriptomics, Visualization Version 1.8.0 In Bioconductor since BioC 3.17 (R-4.3) (2 years) 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 Linking To Enhances Depends On Me Imports Me Suggests Me Links To Me Build Report Build Report Package Archives

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

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