miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis

Bioinformatics Pipeline

[Pentest] miRanda: An miRNA target scanner that aims to predict mRNA targets for microRNAs using dynamic-programming alignment and thermodynamics

myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry

An open-source and scalable solution to NGS analysis powered by the NIH's Biowulf cluster.

An open-source R package to comprehensively explore the role of impaired miRNA regulatory networks in complex biological conditions.

scripts and resources for performing miRNA sequencing analysis using tools like mirPRo and miRDeep2. Explore the code to process reads, map them to the genome, quantify known miRNAs, identify novel miRNAs, and browse the results

miRSim Synthetic Sequence Simulator

An awesome microRNA-sequencing pipeline

Scripts of Final Master Project

This is an automated Bash pipeline for reproducible miRNA analysis from miRBase v22. I used C. elegans (lin-4/let-7) precursors using SeqKit for biochemical metric extraction.

R package to predict gene feed forward loops using mediation analysis. Analyses integrate observed miRNA and mRNA expression data and database information on gene interactions.

multiMiR package in R, providing gene-miRNA-lncRNA interactions for ceRNA network construction

This is a complete Nextflow pipeline to analyse, process and align deep sequencing miRNA reads.

This repository demonstrates an independent analysis of miRNA differential expression in Pancreatic Ductal Adenocarcinoma (PDAC), using publicly available datasets.

All the R scripts I used during my time as a grad student at Clemson University

Interactive Shiny app for miRNA differential expression analysis, visualization, enrichment, machine learning classification, and power analysis — built for researchers and bioinformaticians