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

Functions

Borda Man page
BordaTopk Man page
bRank Man page
convert Man page
Dcov Man page
DiffExpAnalysis Man page
Elastic Man page
experiment Man page
Extopk Man page
filterAndCompare Man page
getData Man page
GOBPenrichment Man page
Hoeffding Man page
IDA Man page
ImputeNormData Man page
KEGGenrichment Man page
Kendall Man page
Lasso Man page
MI Man page
miRLAB Man page
miRLAB-package Man page
Pearson Man page
ProMISe Man page
RDC Man page
Read Man page
ReadExtResult Man page
readHeader Man page
Spearman Man page
Standardise Man page
ValidateAll Man page
Validation Man page
ValidationT Man page
Zscore Man page

Files

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.

Please suggest features or report bugs with the GitHub issue tracker.

All documentation is copyright its authors; we didn't write any of that.