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.

AuthorThuc Duy Le, Junpeng Zhang
Date of publicationNone
MaintainerThuc Duy Le <Thuc.Le@unisa.edu.au>
LicenseGPL (>=2)
Version1.4.0

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

Questions? Problems? Suggestions? or email at ian@mutexlabs.com.

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