miRLAB: Dry lab for exploring miRNA-mRNA relationships
Version 1.6.0

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
Bioconductor views GeneExpression Network NetworkInference miRNA
Date of publicationNone
MaintainerThuc Duy Le <Thuc.Le@unisa.edu.au>
LicenseGPL (>=2)
Version1.6.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("miRLAB")

Getting started

Package overview
miRLAB

Popular man pages

Borda: Ensemble method for miRNA target prediction using Borda count...
convert: Convert miRNA symbols from a miRBase version to another
Elastic: miRNA target prediction with the Elastic-net regression...
KEGGenrichment: Functional enrichment analysis KEGG enrichment analysis for a...
Lasso: miRNA target prediction with the Lasso method
miRLAB-package: A dry lab for exploring miRNA-mRNA relationships
Pearson: miRNA target prediction with the Pearson correlation...
See all...

All man pages Function index File listing

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

Functions

Borda Man page Source code
BordaTopk Man page Source code
CheckGeneSymbol Source code
CombineMultiPlatformData Source code
CombineRedundantFeature Source code
Dcov Man page Source code
DiffExpAnalysis Man page Source code
DownloadRNASeqData Source code
DownloadmiRNASeqData Source code
EMI Source code
Elastic Man page Source code
Extopk Man page Source code
GOBPenrichment Man page Source code
GetNewestURL Source code
Hoeffding Man page Source code
IDA Man page Source code
ImputeNormData Man page Source code
KEGGenrichment Man page Source code
Kendall Man page Source code
Lasso Man page Source code
MI Man page Source code
Pearson Man page Source code
ProMISe Man page Source code
ProcessRNASeqData Source code
ProcessmiRNASeqData Source code
RDC Man page Source code
RDCParameter Source code
ReOrder Source code
Read Man page Source code
ReadExtResult Man page Source code
Spearman Man page Source code
Standardise Man page Source code
ToPatientData Source code
ValidateAll Man page Source code
Validation Man page Source code
ValidationT Man page Source code
Zscore Man page Source code
bRank Man page Source code
convert Man page Source code
experiment Man page Source code
filterAndCompare Man page Source code Source code
getData Man page Source code
grepBeginning Source code
grepEnd Source code
miRLAB Man page
miRLAB-package Man page
queryTargetFile Source code
readHeader Man page Source code
urlReadTable Source code

Files

DESCRIPTION
NAMESPACE
R
R/miRLAB.R
build
build/vignette.rds
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/miRLAB-vignette.R
inst/doc/miRLAB-vignette.Rmd
inst/doc/miRLAB-vignette.html
inst/extdata
inst/extdata/MINE.jar
inst/extdata/ToyEMT.csv
inst/extdata/Toygroundtruth.csv
inst/extdata/ToymiRs.csv
inst/extdata/Transfection_data_summary.csv
inst/extdata/database.RData
inst/unitTests
inst/unitTests/test_Pearson.R
man
man/Borda.Rd
man/BordaTopk.Rd
man/Dcov.Rd
man/DiffExpAnalysis.Rd
man/Elastic.Rd
man/Extopk.Rd
man/GOBPenrichment.Rd
man/Hoeffding.Rd
man/IDA.Rd
man/ImputeNormData.Rd
man/KEGGenrichment.Rd
man/Kendall.Rd
man/Lasso.Rd
man/MI.Rd
man/Pearson.Rd
man/ProMISe.Rd
man/RDC.Rd
man/Read.Rd
man/ReadExtResult.Rd
man/Spearman.Rd
man/Standardise.Rd
man/ValidateAll.Rd
man/Validation.Rd
man/ValidationT.Rd
man/Zscore.Rd
man/bRank.Rd
man/convert.Rd
man/experiment.Rd
man/filterAndCompare.Rd
man/getData.Rd
man/miRLAB-package.Rd
man/readHeader.Rd
tests
tests/runTests.R
vignettes
vignettes/miRLAB-vignette.Rmd
miRLAB documentation built on May 20, 2017, 10:53 p.m.

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