SPONGE
This is the development version of SPONGE; for the stable release version, see SPONGE.
Sparse Partial Correlations On Gene Expression
Bioconductor version: Development (3.21)
This package provides methods to efficiently detect competitive endogeneous RNA interactions between two genes. Such interactions are mediated by one or several miRNAs such that both gene and miRNA expression data for a larger number of samples is needed as input. The SPONGE package now also includes spongEffects: ceRNA modules offer patient-specific insights into the miRNA regulatory landscape.
Author: Markus List [aut, cre] (ORCID:
Maintainer: Markus List <markus.list at tum.de>
citation("SPONGE")):
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("SPONGE")
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("SPONGE")| SPONGE vignette | HTML | R Script |
| spongEffects vignette | HTML | R Script |
| Reference Manual | ||
| NEWS | Text |
Details
| biocViews | GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics |
| Version | 1.29.0 |
| In Bioconductor since | BioC 3.6 (R-3.4) (7 years) |
| License | GPL (>=3) |
| Depends | R (>= 3.6) |
| Imports | Biobase, stats, ppcor, logging, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, tidyverse, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr |
| System Requirements | |
| URL |
See More
| Suggests | testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA |
| Linking To | |
| Enhances | |
| Depends On Me | |
| Imports Me | miRspongeR |
| Suggests Me | mirTarRnaSeq |
| Links To Me | |
| Build Report | Build Report |
Package Archives
Follow Installation instructions to use this package in your R session.
| Source Package | SPONGE_1.29.0.tar.gz |
| Windows Binary (x86_64) | SPONGE_1.29.0.zip |
| macOS Binary (x86_64) | SPONGE_1.29.0.tgz |
| macOS Binary (arm64) | SPONGE_1.29.0.tgz |
| Source Repository | git clone https://git.bioconductor.org/packages/SPONGE |
| Source Repository (Developer Access) | git clone git@git.bioconductor.org:packages/SPONGE |
| Bioc Package Browser | https://code.bioconductor.org/browse/SPONGE/ |
| Package Short Url | https://bioconductor.org/packages/SPONGE/ |
| Package Downloads Report | Download Stats |