ceRNAnetsim
This is the development version of ceRNAnetsim; for the stable release version, see ceRNAnetsim.
Regulation Simulator of Interaction between miRNA and Competing RNAs (ceRNA)
Bioconductor version: Development (3.24)
This package simulates regulations of ceRNA (Competing Endogenous) expression levels after a expression level change in one or more miRNA/mRNAs. The methodolgy adopted by the package has potential to incorparate any ceRNA (circRNA, lincRNA, etc.) into miRNA:target interaction network. The package basically distributes miRNA expression over available ceRNAs where each ceRNA attracks miRNAs proportional to its amount. But, the package can utilize multiple parameters that modify miRNA effect on its target (seed type, binding energy, binding location, etc.). The functions handle the given dataset as graph object and the processes progress via edge and node variables.
Author: Selcen Ari Yuka [aut, cre]
, Alper Yilmaz [aut]
Maintainer: Selcen Ari Yuka <selcenarii at gmail.com>
citation("ceRNAnetsim")):
Huber W, Carey VJ, Gentleman R, Anders S, Carlson M, Carvalho BS, Bravo HC, Davis S, Gatto L, Girke T, Gottardo R, Hahne F, Hansen KD, Irizarry RA, Lawrence M, Love MI, MacDonald J, Obenchain V, Oleś AK, Pagès H, Reyes A, Shannon P, Smyth GK, Tenenbaum D, Waldron L, Morgan M (2015). "Orchestrating high-throughput genomic analysis with Bioconductor." Nature Methods, 12(2), 115–121. doi:10.1038/nmeth.3252.
Gentleman RC, Carey VJ, Bates DM, Bolstad B, Dettling M, Dudoit S, Ellis B, Gautier L, Ge Y, Gentry J, Hornik K, Hothorn T, Huber W, Iacus S, Irizarry R, Leisch F, Li C, Maechler M, Rossini AJ, Sawitzki G, Smith C, Smyth G, Tierney L, Yang JYH, Zhang J (2004). "Bioconductor: open software development for computational biology and bioinformatics." Genome Biology, 5(10), R80. doi:10.1186/gb-2004-5-10-r80.
Installation
To install this package, start R (version "4.6") and enter:
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
## The following initializes the development version of Bioconductor
BiocManager::install(version = "devel")
BiocManager::install("ceRNAnetsim")
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("ceRNAnetsim")| A Suggestion: How to Find the Appropriate Iteration for Simulation | HTML | R Script |
| An TCGA dataset application | HTML | R Script |
| auxiliary_commands | HTML | R Script |
| basic_usage | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GraphAndNetwork, Network, NetworkInference, Software, SystemsBiology, Transcriptomics |
| Version | 1.25.0 |
| In Bioconductor since | BioC 3.11 (R-4.0) (6.5 years) |
| License | GPL (>= 3.0) |
| Depends | R (>= 4.0.0), dplyr, tidygraph |
| Imports | furrr, rlang, tibble, ggplot2, ggraph, igraph, purrr, tidyr, future, stats |
| System Requirements | |
| URL | https://github.com/selcenari/ceRNAnetsim |
| Bug Reports | https://github.com/selcenari/ceRNAnetsim/issues |
See More
| Suggests | knitr, png, rmarkdown, testthat, covr |
| 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 | ceRNAnetsim_1.25.0.tar.gz |
| Windows Binary (x86_64) | ceRNAnetsim_1.25.0.zip |
| macOS Binary (big-sur-x86_64) | ceRNAnetsim_1.25.0.tgz |
| macOS Binary (sonoma-arm64) | ceRNAnetsim_1.25.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/ceRNAnetsim |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/ceRNAnetsim |
| Bioc Package Browser | https://code.bioconductor.org/browse/ceRNAnetsim/ |
| Package Short Url | https://bioconductor.org/packages/ceRNAnetsim/ |
| Package Downloads Report | Download Stats |