mastR
This is the development version of mastR; for the stable release version, see mastR.
Markers Automated Screening Tool in R
Bioconductor version: Development (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:
Maintainer: Jinjin Chen <chen.j at wehi.edu.au>
citation("mastR")):
Installation
To install this package, start R (version "4.5") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
# The following initializes usage of Bioc devel
BiocManager::install(version='devel')
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 | ||
| NEWS | Text | |
| LICENSE | Text |
Details
| biocViews | DifferentialExpression, GeneExpression, Software, Transcriptomics, Visualization |
| Version | 1.7.0 |
| In Bioconductor since | BioC 3.17 (R-4.3) (1.5 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.
| Source Package | mastR_1.7.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| 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 |