Package: miRLAB 1.35.0

Thuc Duy Le

miRLAB: Dry lab for exploring miRNA-mRNA relationships

Provide tools exploring miRNA-mRNA relationships, including popular miRNA target prediction methods, ensemble methods that integrate individual methods, functions to get data from online resources, functions to validate the results, and functions to conduct enrichment analyses.

Authors:Thuc Duy Le, Junpeng Zhang, Mo Chen, Vu Viet Hoang Pham

miRLAB_1.35.0.tar.gz

miRLAB_1.35.0.tar.gz(r-4.5-noble)miRLAB_1.35.0.tar.gz(r-4.4-noble)
miRLAB_1.35.0.tgz(r-4.4-emscripten)miRLAB_1.35.0.tgz(r-4.3-emscripten)
miRLAB.pdf |miRLAB.html✨
miRLAB/json (API)
NEWS

# Install 'miRLAB' in R:

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

Bug tracker:https://github.com/pvvhoang/mirlab/issues

On BioConductor:miRLAB-1.35.0(bioc 3.20)miRLAB-1.34.0(bioc 3.19)

bioconductor-package

32 exports 1.00 score 187 dependencies

Last updated 2 months agofrom:71301a02b0

Exports:Borda BordaTopk bRank convert Dcov DiffExpAnalysis Elastic experiment Extopk filterAndCompare getData GOBPenrichment Hoeffding ICPPam50 IDA identifymiRTargetsByEnsemble identifymiRTargetsByICPPam50 ImputeNormData KEGGenrichment Kendall Lasso MI Pearson RDC Read ReadExtResult readHeader Spearman ValidateAll Validation ValidationT Zscore

Dependencies:abind amap annotate AnnotationDbi AnnotationForge askpass backports base64enc bdsmatrix BH Biobase BiocFileCache BiocGenerics BiocManager biomaRt Biostrings bit bit64 bitops blob boot bslib cachem Category caTools checkmate cli clipr clue cluster codetools colorspace corpcor cpp11 crayon ctc curl data.table DBI dbplyr DelayedArray DEoptimR digest downloader dplyr energy entropy evaluate fansi farver fastICA fastmap filelock fontawesome foreach foreign Formula fs genefilter generics GenomeInfoDb GenomeInfoDbData GenomicRanges ggm ggplot2 glmnet glue GO.db GOstats gplots graph gridExtra GSEABase gsl gtable gtools highr Hmisc hms htmlTable htmltools htmlwidgets httr httr2 igraph impute inum InvariantCausalPrediction IRanges isoband iterators jquerylib jsonlite KEGGREST KernSmooth knitr labeling lattice libcoin lifecycle limma lmtest magrittr MASS Matrix MatrixGenerics matrixStats mboost memoise mgcv mime munsell mvtnorm nlme nnet nnls openssl org.Hs.eg.db partykit pcalg pillar pkgconfig plogr plyr png prettyunits progress purrr quadprog R.methodsS3 R.oo R.utils R6 rappdirs RBGL RColorBrewer Rcpp RcppArmadillo RcppEigen RCurl readr Rgraphviz rlang rmarkdown robustbase rpart RSQLite rstudioapi rvest S4Arrays S4Vectors sass scales selectr sfsmisc shape SparseArray stabs statmod stringi stringr SummarizedExperiment survival sys TCGAbiolinks TCGAbiolinksGUI.data tibble tidyr tidyselect tinytex tzdb UCSC.utils utf8 vcd vctrs viridis viridisLite vroom withr xfun XML xml2 xtable XVector yaml zlibbioc zoo

miRLAB

Thuc Duy Le

Rendered frommiRLAB-vignette.Rmdusingknitr::rmarkdownon Jun 30 2024.

Last update: 2021-10-07
Started: 2015-07-16

Citation

Development and contributors

Readme and manuals

Help Manual

Help page	Topics
A dry lab for exploring miRNA-mRNA relationships	miRLAB-package miRLAB
Ensemble method for miRNA target prediction using Borda count election	Borda
Ensemble method for miRNA target prediction using Borda count election with topk targets	BordaTopk
Extract topk predicted targets of a miRNA Rank all the targets of a miRNA and extract the topk targets	bRank
Convert miRNA symbols from a miRBase version to another	convert
miRNA target prediction with the Distance correlation method	Dcov
Differentially expressed analysis	DiffExpAnalysis
miRNA target prediction with the Elastic-net regression coefficient method	Elastic
Function for validate the results from all 12 methods.	experiment
Extract top k miRNA-mRNA interactions	Extopk
Filter and compare the validation results from 12 methods Keep the miRNAs that have at least noVal confirmed targets and compare the validation results from all methods.	filterAndCompare
getData from GDC	getData
Functional enrichment analysis	GOBPenrichment
miRNA target prediction with the Hoeffding correlation coefficient method	Hoeffding
Identify miRNA targets by ICP and PAM50	ICPPam50
miRNA target prediction with the IDA method	IDA
Identify the top miRNA targets by an ensemble method with ICP-PAM50, Pearson and Lasso	identifymiRTargetsByEnsemble
Identify the top miRNA targets by ICP and PAM50	identifymiRTargetsByICPPam50
Filter, impute, and normalise data.	ImputeNormData
Functional enrichment analysis KEGG enrichment analysis for a gene list	KEGGenrichment
miRNA target prediction with the Kendall correlation coefficient method	Kendall
miRNA target prediction with the Lasso method	Lasso
miRNA target prediction with mutual information method	MI
miRNA target prediction with the Pearson correlation coefficient method	Pearson
miRNA target prediction with the Randomized Dependence Coefficient method	RDC
Read dataset from csv file	Read
Read results from other methods	ReadExtResult
Read the header of the dataset	readHeader
miRNA target prediction with the Spearman correlation coefficient method	Spearman
Stardarsise the dataset Stadardise the dataset to have mean=0 and std=1 in each column.	Standardise
Validate the targets of all miRNA using both experimentally confirmed and transfection data	ValidateAll
Validate the targets of a miRNA	Validation
Validate the targets of a miRNA using transfection data	ValidationT
miRNA target prediction with the Z-score method	Zscore