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miRLAB (version 1.2.2)

Dry lab for exploring miRNA-mRNA relationships

Description

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.

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Version

Version

1.2.2

License

GPL (>=2)

Maintainer

Thuc Duy Le

Last Published

February 15th, 2017

Functions in miRLAB (1.2.2)

GOBPenrichment

Functional enrichment analysis
BordaTopk

Ensemble method for miRNA target prediction using Borda count election with topk targets
ProMISe

miRNA target prediction with the ProMISe method
Dcov

miRNA target prediction with the Distance correlation method
Extopk

Extract top k miRNA-mRNA interactions
KEGGenrichment

Functional enrichment analysis KEGG enrichment analysis for a gene list
RDC

miRNA target prediction with the Randomized Dependence Coefficient method
readHeader

Read the header of the dataset
Read

Read dataset from csv file
Elastic

miRNA target prediction with the Elastic-net regression coefficient method
bRank

Extract topk predicted targets of a miRNA Rank all the targets of a miRNA and extract the topk targets
Standardise

Stardarsise the dataset Stadardise the dataset to have mean=0 and std=1 in each column.
Zscore

miRNA target prediction with the Z-score method
miRLAB-package

A dry lab for exploring miRNA-mRNA relationships
ValidationT

Validate the targets of a miRNA using transfection data
MI

miRNA target prediction with mutual information method
filterAndCompare

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.
ValidateAll

Validate the targets of all miRNA using both experimentally confirmed and transfection data
convert

Convert miRNA symbols from a miRBase version to another
Spearman

miRNA target prediction with the Spearman correlation coefficient method
DiffExpAnalysis

Differentially expressed analysis
Validation

Validate the targets of a miRNA
Hoeffding

miRNA target prediction with the Hoeffding correlation coefficient method
getData

Get data from TCGA
experiment

Function for validate the results from all 12 methods.
Borda

Ensemble method for miRNA target prediction using Borda count election
ImputeNormData

Filter, impute, and normalise data.
IDA

miRNA target prediction with the IDA method
Kendall

miRNA target prediction with the Kendall correlation coefficient method
ReadExtResult

Read results from other methods
Lasso

miRNA target prediction with the Lasso method
Pearson

miRNA target prediction with the Pearson correlation coefficient method