miRLAB: Dry lab for exploring miRNA-mRNA relationships

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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.

Author
Thuc Duy Le, Junpeng Zhang
Date of publication
None
Maintainer
Thuc Duy Le <Thuc.Le@unisa.edu.au>
License
GPL (>=2)
Version
1.4.0

View on Bioconductor

Man pages

Borda
Ensemble method for miRNA target prediction using Borda count...
BordaTopk
Ensemble method for miRNA target prediction using Borda count...
bRank
Extract topk predicted targets of a miRNA Rank all the...
convert
Convert miRNA symbols from a miRBase version to another
Dcov
miRNA target prediction with the Distance correlation method
DiffExpAnalysis
Differentially expressed analysis
Elastic
miRNA target prediction with the Elastic-net regression...
experiment
Function for validate the results from all 12 methods.
Extopk
Extract top k miRNA-mRNA interactions
filterAndCompare
Filter and compare the validation results from 12 methods...
getData
Get data from TCGA
GOBPenrichment
Functional enrichment analysis
Hoeffding
miRNA target prediction with the Hoeffding correlation...
IDA
miRNA target prediction with the IDA method
ImputeNormData
Filter, impute, and normalise data.
KEGGenrichment
Functional enrichment analysis KEGG enrichment analysis for a...
Kendall
miRNA target prediction with the Kendall correlation...
Lasso
miRNA target prediction with the Lasso method
MI
miRNA target prediction with mutual information method
miRLAB-package
A dry lab for exploring miRNA-mRNA relationships
Pearson
miRNA target prediction with the Pearson correlation...
ProMISe
miRNA target prediction with the ProMISe method
RDC
miRNA target prediction with the Randomized Dependence...
Read
Read dataset from csv file
ReadExtResult
Read results from other methods
readHeader
Read the header of the dataset
Spearman
miRNA target prediction with the Spearman correlation...
Standardise
Stardarsise the dataset Stadardise the dataset to have mean=0...
ValidateAll
Validate the targets of all miRNA using both experimentally...
Validation
Validate the targets of a miRNA
ValidationT
Validate the targets of a miRNA using transfection data
Zscore
miRNA target prediction with the Z-score method

Files in this package

miRLAB/DESCRIPTION
miRLAB/NAMESPACE
miRLAB/R
miRLAB/R/miRLAB.R
miRLAB/build
miRLAB/build/vignette.rds
miRLAB/inst
miRLAB/inst/CITATION
miRLAB/inst/NEWS
miRLAB/inst/doc
miRLAB/inst/doc/miRLAB-vignette.R
miRLAB/inst/doc/miRLAB-vignette.Rmd
miRLAB/inst/doc/miRLAB-vignette.html
miRLAB/inst/extdata
miRLAB/inst/extdata/MINE.jar
miRLAB/inst/extdata/ToyEMT.csv
miRLAB/inst/extdata/Toygroundtruth.csv
miRLAB/inst/extdata/ToymiRs.csv
miRLAB/inst/extdata/Transfection_data_summary.csv
miRLAB/inst/extdata/database.RData
miRLAB/inst/unitTests
miRLAB/inst/unitTests/test_Pearson.R
miRLAB/man
miRLAB/man/Borda.Rd
miRLAB/man/BordaTopk.Rd
miRLAB/man/Dcov.Rd
miRLAB/man/DiffExpAnalysis.Rd
miRLAB/man/Elastic.Rd
miRLAB/man/Extopk.Rd
miRLAB/man/GOBPenrichment.Rd
miRLAB/man/Hoeffding.Rd
miRLAB/man/IDA.Rd
miRLAB/man/ImputeNormData.Rd
miRLAB/man/KEGGenrichment.Rd
miRLAB/man/Kendall.Rd
miRLAB/man/Lasso.Rd
miRLAB/man/MI.Rd
miRLAB/man/Pearson.Rd
miRLAB/man/ProMISe.Rd
miRLAB/man/RDC.Rd
miRLAB/man/Read.Rd
miRLAB/man/ReadExtResult.Rd
miRLAB/man/Spearman.Rd
miRLAB/man/Standardise.Rd
miRLAB/man/ValidateAll.Rd
miRLAB/man/Validation.Rd
miRLAB/man/ValidationT.Rd
miRLAB/man/Zscore.Rd
miRLAB/man/bRank.Rd
miRLAB/man/convert.Rd
miRLAB/man/experiment.Rd
miRLAB/man/filterAndCompare.Rd
miRLAB/man/getData.Rd
miRLAB/man/miRLAB-package.Rd
miRLAB/man/readHeader.Rd
miRLAB/tests
miRLAB/tests/runTests.R
miRLAB/vignettes
miRLAB/vignettes/miRLAB-vignette.Rmd