markeR
This is thereleased version of markeR; for the devel version, seemarkeR.
An R Toolkit for Evaluating Gene Signatures as Phenotypic Markers
Bioconductor version: Release (3.22)
markeR is an R package that provides a modular and extensible framework for the systematic evaluation of gene sets as phenotypic markers using transcriptomic data. The package is designed to support both quantitative analyses and visual exploration of gene set behaviour across experimental and clinical phenotypes. It implements multiple methods, including score-based and enrichment approaches, and also allows the exploration of expression behaviour of individual genes. In addition, users can assess the similarity of their own gene sets against established collections (e.g., those from MSigDB), facilitating biological interpretation.
Author: Rita Martins-Silva [aut, cre]
ORCID: 0000-0002-1067-7993, Alexandre Kaizeler [aut, ctb] ORCID: 0000-0002-9117-6073, Nuno Luís Barbosa-Morais [aut, led, ths] ORCID: 0000-0002-1215-0538
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")BiocManager::install("markeR")For older versions of R, please refer to the appropriateBioconductor 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 | ||
| NEWS | Text |
Details
| biocViews | Classification,GeneExpression,GeneSetEnrichment,Software,Transcriptomics,Visualization |
| Version | 1.0.0 |
| In Bioconductor since | BioC 3.22 (R-4.5) (< 6 months) |
| 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
FollowInstallation instructions to use this package in your R session.
| Source Package | markeR_1.0.0.tar.gz |
| Windows Binary (x86_64) | markeR_1.0.0.zip |
| macOS Binary (x86_64) | markeR_1.0.0.tgz |
| macOS Binary (arm64) | markeR_1.0.0.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 |