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MIRNARIP_1.0.tar.gz
README.md
RNAseqV2_expression_matrix_update_symbols.csv.zip
miRNA_seq_expression_matrix.csv
miRNA_target_gene_TarBase.csv.zip
mirna_candidates_example.txt
mirnarip_manual.pdf
start_MIRNARIP.R
total_experimental_pre_mirna_mapping.csv
total_mature_pre_mirna_mapping.csv

README.md

MIRNA-RIP

MIRNA-RIP: The miRNA Regulatory Interaction Predictor

About MIRNA-RIP

MIRNA-RIP is a software package for R (www.r-project.org) to predict miRNAs as regulators of potential target genes using matched gene- and miRNA expression profiles. MIRNARIP implements two model types using Mixed Integer Linear Programming: simple linear regression and piecewise linear regression. In both model types, specific parameters are optimized to estimate the target gene expression using the expression of the corresponding miRNA. Target gene predictions from both models are summarized in a combined model. More information about installation and usage including an example data set can be found in the manual.

Downloads

MIRNA-RIP 1.0

MIRNA-RIP R package

MIRNA-RIP manual
start_MIRNARIP.R

Example data

Gene expression data, taken from [1]

miRNA expression data, taken from [1]

miRNA – target gene interactions, taken from [2]

miRNA mature2pre-miRNA_ID mapping, extracted from [3]

miRNA experimental2pre-miRNA_ID mapping, extracted from [3]

miRNA candidates

Please cite: Ast et al. MiR-192, miR-200c and miR-17 are fibroblast-mediated inhibitors of colorectal cancer invasion. Oncotarget (2018).

References

The Cancer Genome Atlas Network. Comprehensive Molecular Characterization of Human Colon and Rectal Cancer. Nature. 2012;487(7407):330-337.

Karagkouni et al. DIANA-TarBase v8: a decade-long collection of experimentally supported miRNA–gene interactions. Nucleic Acids Res. 2018 Jan 4; 46(Database issue): D239–D245.

Kozomara and Griffiths-Jones miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Research, Volume 42, Issue D1, 1 January 2014, Pages D68–D73

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