mirna

Discovering known and novel miRNAs from small RNA sequencing data

small RNA analysis from NGS data

An attempt to help anyone interested in using Perl for Bioinformatics

Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs

small rna-seq analysis package

Precursor microRNA Identification Using Deep Convolutional Neural Networks

LncmiRSRN: Identifying lncRNA related miRNA sponge regulatory network

isomiR quantification and analysis pipeline

Using RNA-Seq data to improve microRNA target prediction accuracy in animals

analyze isomiRs from seqbuster tool

A software to detect genome-wide miRNA-gene enrichment signal.

A tool to automate exploratory miRNA prediction in genomes.

NAnostring quality Control dasHbOard

Analyze single-cell miRNA sequencing data from HL-60 cells along a 7-day time-course of ATRA treatment.

A python-based isomiR quantification and analysis pipeline that utilizes a number of recent and novel miRNA biological insights to produce useful analytics

miRNA-UTR approximate matching algorithms in R/Python/Bash

circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data

Simulation of interactions miRNA:Competing Targets

miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information

OmicSelector - Environment, docker-based application and R package for biomarker signiture selection (feature selection) & deep learning diagnostic tool development from high-throughput high-throughput omics experiments and other multidimensional datasets. Initially developed for miRNA-seq, RNA-seq and qPCR.

miRspongeR: identification and analysis of miRNA sponge interaction networks and modules

BioSeq2vec: learning deep representation of biological sequences using LSTM Encoder-Decoder

Small RNAseq pipeline for paired-end reads

Use this program can let user quickly combine the miRNA/Gene expression and clinical data. Speed up the data preprocessing step.

Snakemake pipeline for miRNA and piRNA quantification from QIAseq miRNA Library Kit libraries

Simple scripts to parallelize miRNA analysis with sRNAtoolbox performed for my Master thesis.

A software to predict miRNA secondary structure regarding conformation energy and matching size.

Source code for miRiam web server and visualisation