MIRit
Integrate microRNA and gene expression to decipher pathway complexity
Bioconductor version: 3.23 · Package version: 1.8.0
Other Bioconductor versions
devel is the development version; release is the current stable one.
3.24 (devel), 3.23 (release)
MIRit is an R package that provides several methods for investigating the relationships between miRNAs and genes in different biological conditions. In particular, MIRit allows to explore the functions of dysregulated miRNAs, and makes it possible to identify miRNA-gene regulatory axes that control biological pathways, thus enabling the users to unveil the complexity of miRNA biology. MIRit is an all-in-one framework that aims to help researchers in all the central aspects of an integrative miRNA-mRNA analyses, from differential expression analysis to network characterization.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("MIRit")Details
| Maintainer | Jacopo Ronchi <jacopo.ronchi@unimib.it> |
| Author | Jacopo Ronchi [aut, cre] (ORCID: <https://orcid.org/0000-0001-5520-4631>), Maria Foti [fnd] (ORCID: <https://orcid.org/0000-0002-4481-1900>) |
| License | GPL (>= 3) |
| URL | https://jacopo-ronchi.github.io/MIRit/, https://github.com/jacopo-ronchi/MIRit |
| Bug Reports | https://github.com/jacopo-ronchi/MIRit/issues |
| Source branch | RELEASE_3_23 |
| Build report | Bioconductor build system, r-universe |
| biocViews | DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Network, NetworkEnrichment, NetworkInference, Pathways, Software, SystemsBiology |
| Package Short Url | https://bioconductor.org/packages/MIRit/ |
Citation
From within R, enter citation("MIRit"):
Jacopo Ronchi. MIRit: Integrate microRNA and gene expression to decipher pathway complexity. doi:10.18129/B9.bioc.MIRit, R package version 1.8.0, https://bioconductor.org/packages/MIRit.
Generated from the package metadata; it may differ from the package's own citation.
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | MIRit_1.8.0.tar.gz |
| macOS binary (arm64) | MIRit_1.8.0.tgz |
| macOS binary (x86_64) | MIRit_1.8.0.tgz |
Dependencies
Depends: MultiAssayExperiment, R (>= 4.4.0)
Imports: AnnotationDbi, BiocFileCache, BiocParallel, DESeq2, edgeR, fgsea, genekitr, geneset, ggplot2, ggpubr, graph, graphics, graphite, grDevices, httr, limma, methods, Rcpp, Rgraphviz (>= 2.44.0), rlang, stats, utils
LinkingTo: Rcpp
Suggests: BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0)