mirna

nf-core/circrna

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

junchaoshi/sports1.1

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

lpantano/seqcluster

small RNA analysis from NGS data

biocoder/Perl-for-Bioinformatics

An attempt to help anyone interested in using Perl for Bioinformatics

kstawiski/OmicSelector

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.

dmnfarrell/smallrnaseq

small rna-seq analysis package

gitHBDX/TransfoRNA

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

miRTop/mirtop

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

eandresleon/miARma-seq

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

multitalk/miRTalk

Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data

zhangjunpeng411/LncmiRSRN

LncmiRSRN: Identifying lncRNA related miRNA sponge regulatory network

peace195/miRNA-identification-conv2D

Precursor microRNA Identification Using Deep Convolutional Neural Networks

TBradley27/FilTar

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

HCGB-IGTP/XICRA

Small RNAseq pipeline for paired-end reads

kevinniechen/quagmir

isomiR quantification and analysis pipeline

saorisakaue/MIGWAS

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

sinanugur/MirMachine

MirMachine, a command line tool to detect microRNA homologs in genome sequences.

sing-group/my-brain-seq

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

lpantano/isomiRs

analyze isomiRs from seqbuster tool

mcanouil/NACHO

NAnostring quality Control dasHbOard.

hacktrackgnulinux/miranda

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

tacazares/SeedMatchR

Off-target analysis of siRNA knock down paired with RNAseq

ETHZ-INS/scanMiR

A set of tools for scanning for miRNA binding sites and working with affinity models

jtremblay/MiRNATarget

A command line version of the psRNATarget workflow that predicts potential miRNA target locations on a genome.

lpantano/seqclusterViz

visualization of seqcluster output, try at:

zavolanlab/mirflowz

Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.

ailab-seoultech/deepTarget

gbnegrini/mirdb-custom-target-search

This script implements a Selenium WebDriver to automate the access to miRDB - MicroRNA Target Prediction and Functional Study Database and search for microRNAs targets/seeds present in custom mRNA sequences.

omics-datascience/modulector

An open platform which provides information about miRNAs and genes from different popular databases

selcenari/ceRNAnetsim

Simulation of interactions miRNA:Competing Targets

YannDubs/miRNAseq-Analysis

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

zhangjunpeng411/miRspongeR

Identification and analysis of miRNA sponge regulation

haichengyi/bioseq2vec

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

zhangjunpeng411/miRSM

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

zhangjunpeng411/Scan

Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data