miRLAB-package |
A dry lab for exploring miRNA-mRNA relationships |
Borda |
Ensemble method for miRNA target prediction using Borda count election |
BordaTopk |
Ensemble method for miRNA target prediction using Borda count election with topk targets |
bRank |
Extract topk predicted targets of a miRNA Rank all the targets of a miRNA and extract the topk targets |
Dcov |
miRNA target prediction with the Distance correlation method |
DiffExpAnalysis |
Differentially expressed analysis |
Elastic |
miRNA target prediction with the Elastic-net regression coefficient method |
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 Keep the miRNAs that have at least noVal confirmed targets and compare the validation results from all methods. |
getData |
Get data from TCGA |
GOBPenrichment |
Functional enrichment analysis |
Hoeffding |
miRNA target prediction with the Hoeffding correlation coefficient method |
IDA |
miRNA target prediction with the IDA method |
ImputeNormData |
Filter, impute, and normalise data. |
KEGGenrichment |
Functional enrichment analysis KEGG enrichment analysis for a gene list |
Kendall |
miRNA target prediction with the Kendall correlation coefficient method |
Lasso |
miRNA target prediction with the Lasso method |
MI |
miRNA target prediction with mutual information method |
miRLAB |
A dry lab for exploring miRNA-mRNA relationships |
Pearson |
miRNA target prediction with the Pearson correlation coefficient method |
ProMISe |
miRNA target prediction with the ProMISe method |
RDC |
miRNA target prediction with the Randomized Dependence Coefficient method |
Read |
Read dataset from csv file |
readHeader |
Read the header of the dataset |
Spearman |
miRNA target prediction with the Spearman correlation coefficient method |
Standardise |
Stardarsise the dataset Stadardise the dataset to have mean=0 and std=1 in each column. |
ValidateAll |
Validate the targets of all miRNA using both experimentally confirmed and transfection data |
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 |