Discovering known and novel miRNAs from small RNA sequencing data

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

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

small RNA analysis from NGS data

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.

An attempt to help anyone interested in using Perl for Bioinformatics

small rna-seq analysis package

TransfoRNA: Navigating the Uncertainties of Small RNA Annotation with an Adaptive Machine Learning Strategy

miRTarDS is a microRNA target interaction database, including 1,220,904 MTIs from miRTarbase, miRDB, miRWalk, involving 6,085 genes and 1,261 pre-miRNAs. The MTIs prediction achieved an F1 score of 88% in accurately distinguishing protein-level experimentally (western blot & reporter assay) validated MTIs and predicted MTIs.

command lines tool to annotate miRNAs with a standard mirna/isomir naming

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

LncmiRSRN: Identifying lncRNA related miRNA sponge regulatory network

Precursor microRNA Identification Using Deep Convolutional Neural Networks

isomiR quantification and analysis pipeline

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

NAnostring quality Control dasHbOard

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

analyze isomiRs from seqbuster tool

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

Small RNAseq pipeline for paired-end reads