MIRit
This is the development version of MIRit; for the stable release version, see MIRit.
Integrate microRNA and gene expression to decipher pathway complexity
Bioconductor version: Development (3.21)
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.
Author: Jacopo Ronchi [aut, cre] (ORCID:
Maintainer: Jacopo Ronchi <jacopo.ronchi at unimib.it>
citation("MIRit")):
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("MIRit")
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("MIRit")| Integrate miRNA and gene expression data with MIRit | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | DifferentialExpression, Epigenetics, FunctionalGenomics, GeneExpression, GeneRegulation, Network, NetworkEnrichment, NetworkInference, Pathways, Software, SystemsBiology |
| Version | 1.3.0 |
| In Bioconductor since | BioC 3.19 (R-4.4) (0.5 years) |
| License | GPL (>= 3) |
| 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 |
| System Requirements | |
| URL | https://github.com/jacopo-ronchi/MIRit |
| Bug Reports | https://github.com/jacopo-ronchi/MIRit/issues |
See More
| Suggests | BiocStyle, biomaRt, BSgenome.Hsapiens.UCSC.hg38, GenomicRanges, ggrepel, ggridges, Gviz, gwasrapidd, knitr, MonoPoly, org.Hs.eg.db, rmarkdown, testthat (>= 3.0.0) |
| Linking To | Rcpp |
| 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 | MIRit_1.3.0.tar.gz |
| Windows Binary (x86_64) | |
| macOS Binary (x86_64) | |
| macOS Binary (arm64) | |
| Source Repository | git clone https://git.bioconductor.org/packages/MIRit |
| Source Repository (Developer Access) | git clone [email protected]:packages/MIRit |
| Bioc Package Browser | https://code.bioconductor.org/browse/MIRit/ |
| Package Short Url | https://bioconductor.org/packages/MIRit/ |
| Package Downloads Report | Download Stats |