markeR
This is the development version of markeR; to use it, please install the devel version of Bioconductor.
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Bioconductor version: Development (3.22)
A suite of methods for using gene sets to quantify and evaluate the extent to which a given gene signature marks a specific phenotype. The package implements various scoring, enrichment and classification approaches, along with tools to compute performance metrics and visualize results, making it a valuable resource for transcriptomics research (bulk RNA-seq).
Author: Rita Martins-Silva [aut, cre]
, Alexandre Kaizeler [aut, ctb]
, Nuno Luís Barbosa-Morais [aut, led, ths]
Maintainer: Rita Martins-Silva <rita.silva at medicina.ulisboa.pt>
citation("markeR")):
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("markeR")
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("markeR")| Introduction to markeR | HTML | R Script |
| Reference Manual |
Details
| biocViews | Classification, GeneExpression, GeneSetEnrichment, Software, Transcriptomics, Visualization |
| Version | 0.99.5 |
| In Bioconductor since | BioC 3.22 (R-4.5) |
| License | Artistic-2.0 |
| Depends | R (>= 4.5.0) |
| Imports | circlize, edgeR, ComplexHeatmap, ggh4x, ggplot2, ggpubr, grid, gridExtra, pROC, RColorBrewer, reshape2, rstatix, scales, stats, utils, fgsea, limma, ggrepel, effectsize, msigdbr, tibble |
| System Requirements | |
| URL | https://diseasetranscriptomicslab.github.io/markeR/ https://github.com/DiseaseTranscriptomicsLab/markeR |
| Bug Reports | https://github.com/DiseaseTranscriptomicsLab/markeR/issues |
See More
| Suggests | devtools, markdown, renv, testthat, BiocManager, knitr, rmarkdown, roxygen2, mockery, covr, magick, BiocStyle |
| 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 | markeR_0.99.5.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | markeR_0.99.5.tgz |
| macOS Binary (arm64) | markeR_0.99.5.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/markeR |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/markeR |
| Bioc Package Browser | https://code.bioconductor.org/browse/markeR/ |
| Package Short Url | https://bioconductor.org/packages/markeR/ |
| Package Downloads Report | Download Stats |