miRLAB v1.2.2

by Thuc Duy Le

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.

Functions in miRLAB

Name Description
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
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Details

Type Package
Date 2016-01-05
License GPL (>=2)
VignetteBuilder knitr
biocViews miRNA, GeneExpression, NetworkInference, Network

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