Package: miRspongeR 2.9.0

Junpeng Zhang

miRspongeR: Identification and analysis of miRNA sponge regulation

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.

Authors:Junpeng Zhang

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miRspongeR.pdf |miRspongeR.html✨
miRspongeR/json (API)
NEWS

# Install 'miRspongeR' in R:

install.packages('miRspongeR', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org'))

Bug tracker:https://github.com/zhangjunpeng411/mirsponger/issues

On BioConductor:miRspongeR-2.9.0(bioc 3.20)miRspongeR-2.8.0(bioc 3.19)

bioconductor-package

10 exports 0.82 score 266 dependencies 2 mentions

Last updated 2 months agofrom:6e3455f0b7

Exports:integrateMethod moduleDEA moduleFEA moduleSurvival netModule querymiRTargetbinding sample_cor_network sponge_sample_specific spongeMethod spongeValidate

Dependencies:abind AnnotationDbi ape aplot askpass backports base64enc bayestestR BH Biobase BiocFileCache BiocGenerics BiocParallel biomaRt Biostrings bit bit64 blob boot broom bslib cachem callr car carData caret cellranger checkmate circlize class cli clipr clock clue cluster clusterProfiler codetools colorspace ComplexHeatmap conflicted corpcor corrplot cowplot cpp11 crayon curl cvms data.table datawizard DBI dbplyr Deriv diagram digest doBy doParallel doRNG DOSE downloader dplyr dtplyr dynamicTreeCut e1071 ellipsis enrichplot evaluate expm fansi farver fastmap fastmatch fgsea filelock fontawesome forcats foreach formatR fs futile.logger futile.options future future.apply gargle generics GenomeInfoDb GenomeInfoDbData GetoptLong ggforce ggfun ggnewscale ggplot2 ggplotify ggpubr ggraph ggrepel ggridges ggsci ggsignif ggtree glmnet GlobalOptions globals glue GO.db googledrive googlesheets4 GOSemSim gower graph graphite graphlayouts gRbase gridExtra gridGraphics groupdata2 gson gtable hardhat haven HDO.db highr hms htmltools httr httr2 ids igraph insight ipred IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lambda.r lattice lava lazyeval lifecycle linkcomm listenv lme4 logging lubridate magrittr MASS Matrix MatrixModels matrixStats MCL memoise MetBrewer mgcv microbenchmark mime minqa miRBaseConverter ModelMetrics modelr MuMIn munsell nlme nloptr nnet numbers numDeriv openssl org.Hs.eg.db parallelly parameters patchwork pbkrtest pillar pkgconfig plogr plyr png polyclip polynom ppcor prettyunits pROC processx prodlim progress progressr proxy ps purrr quantreg qvalue R6 ragg randomForest rappdirs RColorBrewer Rcpp RcppArmadillo RcppEigen reactome.db ReactomePA readr readxl rearrr recipes rematch rematch2 reprex reshape2 rjson rlang rmarkdown rngtools rpart RSQLite rstatix rstudioapi rvest S4Vectors sass scales scatterpie selectr shadowtext shape snow SparseM SPONGE SQUAREM stringi stringr survival sys systemfonts textshaping tibble tidygraph tidyr tidyselect tidytree tidyverse timechange timeDate tinytex tnet treeio tweenr tzdb UCSC.utils utf8 uuid vctrs viridis viridisLite vroom withr xfun xml2 XVector yaml yulab.utils zlibbioc

Identification and analysis of miRNA sponge regulation

Junpeng Zhang ([email protected]) School of Engineering, Dali University

Rendered frommiRspongeR.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2022-09-22
Started: 2019-03-05

Help page	Topics
Integrate method for identifying miRNA sponge interactions by integrating different methods	integrateMethod
Disease enrichment analysis of modules	moduleDEA
Functional GO, KEGG and Reactome enrichment analysis of modules	moduleFEA
Survival analysis of modules	moduleSurvival
Identifying miRNA sponge modules from network	netModule
A null model for testing purposes in SPONGE R package	precomputed_null_model
Query miRNA-target interactions by combining expression data and putative miRNA-target interactions	querymiRTargetbinding
Identifying sample-sample correlation network	sample_cor_network
Identifying sample-specific miRNA sponge interactions	sponge_sample_specific
Identifying miRNA sponge interactions	spongeMethod
Validation of computationally predicted miRNA sponge interactions	spongeValidate

Package: miRspongeR 2.9.0

miRspongeR: Identification and analysis of miRNA sponge regulation

Identification and analysis of miRNA sponge regulation

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