SPONGE
Sparse Partial Correlations On Gene Expression
Bioconductor version: 3.23 · Package version: 1.34.1
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.
Installation
if (!require("BiocManager", quietly = TRUE))
install.packages("BiocManager")
BiocManager::install("SPONGE")Details
| Maintainer | Markus List <markus.list@tum.de> |
| Author | Markus List [aut, cre] (ORCID: <https://orcid.org/0000-0002-0941-4168>), Markus Hoffmann [aut] (ORCID: <https://orcid.org/0000-0002-1920-288X>), Lena Strasser [aut] (ORCID: <https://orcid.org/0009-0007-7881-6818>), Fabio Boniolo [aut], Azim Dehghani Amirabad [aut], Dennis Kostka [aut], Marcel H. Schulz [aut] |
| License | GPL (>=3) |
| Downloads rank | 587 |
| Source branch | RELEASE_3_23 |
| biocViews | GeneExpression, GeneRegulation, MachineLearning, NetworkInference, RandomForest, Regression, Software, SystemsBiology, Transcription, Transcriptomics |
Documentation
Download
Follow the installation instructions to use this package in your R session.
| Source package | SPONGE_1.34.1.tar.gz |
| Windows binary (x86_64) | SPONGE_1.34.1.zip |
| macOS binary (arm64) | SPONGE_1.34.1.tgz |
| macOS binary (x86_64) | SPONGE_1.34.1.tgz |
Dependencies
Depends: R (>= 3.6)
Imports: methods, Biobase, stats, ppcor, logger, foreach, doRNG, data.table, MASS, expm, gRbase, glmnet, igraph, iterators, caret, dplyr, biomaRt, randomForest, ggridges, cvms, ComplexHeatmap, ggplot2, MetBrewer, rlang, tnet, ggpubr, stringr, tidyr, tibble
Suggests: testthat, knitr, rmarkdown, visNetwork, ggrepel, gridExtra, digest, doParallel, bigmemory, GSVA