Package: miRspongeR
Type: Package
Title: Identification and analysis of miRNA sponge regulation
Version: 2.14.1
Authors@R: 
    person(given = "Junpeng", 
           family = "Zhang", 
           role=c("aut", "cre"), 
           email = "zjp@dali.edu.cn")
Description: This package provides several functions to explore miRNA
        sponge (also called ceRNA or miRNA decoy) regulation from
        putative miRNA-target interactions or/and transcriptomics data
        (including bulk, single-cell and spatial gene expression data).
        It provides eight popular methods for identifying miRNA sponge
        interactions, and an integrative method to integrate miRNA
        sponge interactions from different methods, as well as the
        functions to validate miRNA sponge interactions, and infer
        miRNA sponge modules, conduct enrichment analysis of miRNA
        sponge modules, and conduct survival analysis of miRNA sponge
        modules. By using a sample control variable strategy, it
        provides a function to infer sample-specific miRNA sponge
        interactions. In terms of sample-specific miRNA sponge
        interactions, it implements three similarity methods to
        construct sample-sample correlation network.
Depends: R (>= 4.4.0)
License: GPL-3
URL: <https://github.com/zhangjunpeng411/miRspongeR>
Encoding: UTF-8
biocViews: GeneExpression, BiomedicalInformatics, NetworkEnrichment,
        Survival, Microarray, Software, SingleCell, Spatial, RNASeq
RoxygenNote: 7.3.2
Imports: corpcor, SPONGE, parallel, igraph, MCL, clusterProfiler,
        ReactomePA, DOSE, survival, grDevices, graphics, stats, utils,
        Rcpp, RColorBrewer, grid, org.Hs.eg.db, foreach, doParallel
Suggests: BiocStyle, knitr, rmarkdown, testthat
VignetteBuilder: knitr
BugReports: https://github.com/zhangjunpeng411/miRspongeR/issues
Config/pak/sysreqs: libcairo2-dev cmake libfontconfig1-dev
        libfreetype6-dev libfribidi-dev libglpk-dev make
        libharfbuzz-dev libicu-dev libjpeg-dev libpng-dev libtiff-dev
        libwebp-dev libxml2-dev libssl-dev perl libx11-dev zlib1g-dev
Repository: https://bioc-release.r-universe.dev
Date/Publication: 2025-12-23 12:14:05 UTC
RemoteUrl: https://github.com/bioc/miRspongeR
RemoteRef: RELEASE_3_22
RemoteSha: 8f4bf2441252e181b7fdbbc734ca4c023ff9f7cb
NeedsCompilation: yes
Packaged: 2025-12-24 04:15:15 UTC; root
Author: Junpeng Zhang [aut, cre]
Maintainer: Junpeng Zhang <zjp@dali.edu.cn>
Built: R 4.5.2; x86_64-w64-mingw32; 2025-12-24 04:19:10 UTC; windows
Archs: x64
