mirna

There are 3 repositories under mirna topic.

rajewsky-lab / mirdeep2
Discovering known and novel miRNAs from small RNA sequencing data
mirna microrna smallrna sequencing analysis prediction quantification mapping
Language:Perl 154
nf-core / circrna
circRNA quantification, differential expression analysis and miRNA target prediction of RNA-Seq data
circrna circrna-prediction circrna-pipeline circular-rna rna-seq nf-core nextflow pipeline workflow bioinformatics ngs genomics mirna mirna-targets
Language:Nextflow 54
junchaoshi / sports1.1
Small non-coding RNA annotation Pipeline Optimized for rRNA- and tRNA-Derived Small RNAs
small-rna rna-seq-analysis rna-seq-mapping trna-derived-small-rna rrna-derived-small-rna mirna pirna tsrna rsrna modification trf trna-halves trna-fragment
Language:Perl 50
lpantano / seqcluster
small RNA analysis from NGS data
smallrna mirna trna report sequencing
Language:HTML 37
biocoder / Perl-for-Bioinformatics
An attempt to help anyone interested in using Perl for Bioinformatics
bioinformatics pipeline perl ncrna lncrna mirna
Language:Python 34
OmicSelector
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.
feature-selection omics r r-package classification data-science data-mining bioinformatics bioinformatics-pipeline biomarkers biomarker-discovery docker-image variable-selection deep-learning deep-neural-networks next-generation-sequencing neural-network rna-seq qpcr mirna
Language:R 34
dmnfarrell / smallrnaseq
small rna-seq analysis package
rna-seq smallrna genomics mirna python bioinformatics sequencing
Language:Python 29
gitHBDX / TransfoRNA
TransfoRNA: Navigating the Uncertainties of Small RNA Annotation with an Adaptive Machine Learning Strategy
bioinformatics language-model mirna ngs-analysis rna srna transformer
Language:Python 21
AltasChen / miRTarDS
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 0.889 in accurately distinguishing protein-level experimentally (western blot & reporter assay) validated MTIs and predicted MTIs.
bioinformatics database microrna-target-prediction mirna
Language:Python 20
miRTop / mirtop
command lines tool to annotate miRNAs with a standard mirna/isomir naming
mirna isomirs formatter gff smallrna-seq
Language:Python 18
eandresleon / miARma-seq
miARma-seq: a comprehensive tool for miRNA, mRNA and circRNA analysis
rnaseq-pipeline rna-seq-analysis mirna mirna-seq circrna-pipeline
Language:Perl 14
zhangjunpeng411 / LncmiRSRN
LncmiRSRN: Identifying lncRNA related miRNA sponge regulatory network
lncrna mirna cerna sponge
Language:R 13
peace195 / miRNA-identification-conv2D
Precursor microRNA Identification Using Deep Convolutional Neural Networks
convnet convolutional-neural-networks mirna-identification mirna mirna-secondary-structure pytorch pre-mirna
Language:Python 11
kevinniechen / quagmir
isomiR quantification and analysis pipeline
mirna sequencing pipeline cancer-genomics-cloud
Language:Python 9
multitalk / miRTalk
Extracellular vesicle-derived miRNA-mediated cell-cell communication inference for single-cell transcriptomic data
cell-cell-communication cell-cell-interaction extracellular-vesicles mirna scrna-seq-data single-cell-rna-seq exosomes microvesicles
Language:HTML 9
sing-group / my-brain-seq
myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry
compi differential-expression docker mirna mirna-seq pipeline
Language:R 9
lpantano / isomiRs
analyze isomiRs from seqbuster tool
bioconductor isomirs analyze-isomirs r mirna
Language:R 8
NACHO
mcanouil / NACHO
NAnostring quality Control dasHbOard.
nanostring shiny quality-control normalisation r-package r-stats rstats mirna mrna
Language:R 8
saorisakaue / MIGWAS
A software to detect genome-wide miRNA-gene enrichment signal.
bioinformatics mirna
Language:Python 8
TBradley27 / FilTar
Using RNA-Seq data to improve microRNA target prediction accuracy in animals
mirna mirna-mrna-interaction mirna-targets
Language:Python 8
hacktrackgnulinux / miranda
[Tools] miRanda: An miRNA target scanner that aims to predict mRNA targets for microRNAs using dynamic-programming alignment and thermodynamics
micrornas miranda mirna mirna-seq
Language:C 7
HCGB-IGTP / XICRA
Small RNAseq pipeline for paired-end reads
pipeline mirna smallrna-seq python
Language:Python 7
sinanugur / MirMachine
MirMachine, a command line tool to detect microRNA homologs in genome sequences.
bioinformatics covariance-model mirna prediction
Language:Python 7
tacazares / SeedMatchR
Off-target analysis of siRNA knock down paired with RNAseq
deseq2-analysis mirna rna-seq sirna transcriptomics
Language:R 7
scanMiR
ETHZ-INS / scanMiR
A set of tools for scanning for miRNA binding sites and working with affinity models
mirna scanning tdmd
Language:R 6
jtremblay / MiRNATarget
A command line version of the psRNATarget workflow that predicts potential miRNA target locations on a genome.
micro-rna mirna mirna-targets
Language:Python 6
lpantano / seqclusterViz
visualization of seqcluster output, try at:
smallrna-seq smallrna visualization mirna trna-derived-small-rna
Language:JavaScript 6
zavolanlab / mirflowz
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
bioinformatics isomirs mirna snakemake workflow
Language:Python 6
ailab-seoultech / deepTarget
cnns convolutional-neural-networks deep-learning microrna mirna
Language:Python 5
omics-datascience / modulector
An open platform which provides information about miRNAs and genes from different popular databases
multiomix gene-expression mirna-mrna-interaction mrna mirna methylation pubmed
Language:Python 5
YannDubs / miRNAseq-Analysis
Analyze single-cell miRNA sequencing data from HL-60 cells along a 7-day time-course of ATRA treatment.
bioinformatics rna-seq mirna atra-treatment mirnaseq-analysis
Language:R 5
zhangjunpeng411 / miRspongeR
Identification and analysis of miRNA sponge regulation
mirna sponge cerna
Language:R 5
Bohdan-Khomtchouk / Smalls
miRNA-UTR approximate matching algorithms in R/Python/Bash
mirna utr-regions string-algorithms bioinformatics computational-biology approximate-string-matching
Language:Python 4
haichengyi / bioseq2vec
BioSeq2vec: learning deep representation of biological sequences using LSTM Encoder-Decoder
biological-sequences representation-learning sequence-to-sequence lstm encoder-decoder rna-sequence protein-sequence ncrna-protein-interactions lncrna mirna circrnas
Language:Python 4
selcenari / ceRNAnetsim
Simulation of interactions miRNA:Competing Targets
r network-simulator tidygraph tidyverse network-biology mirna tcga cerna
Language:R 4
zhangjunpeng411 / miRSM
miRSM: Inferring miRNA sponge modules by integrating expression data and miRNA-target binding information
mirna mirna-sponge cerna modules mirna-targets
Language:HTML 4

mirna

rajewsky-lab / mirdeep2

nf-core / circrna

junchaoshi / sports1.1

lpantano / seqcluster

biocoder / Perl-for-Bioinformatics

kstawiski / OmicSelector

dmnfarrell / smallrnaseq

gitHBDX / TransfoRNA

AltasChen / miRTarDS

miRTop / mirtop

eandresleon / miARma-seq

zhangjunpeng411 / LncmiRSRN

peace195 / miRNA-identification-conv2D

kevinniechen / quagmir

multitalk / miRTalk

sing-group / my-brain-seq

lpantano / isomiRs

mcanouil / NACHO

saorisakaue / MIGWAS

TBradley27 / FilTar

hacktrackgnulinux / miranda

HCGB-IGTP / XICRA

sinanugur / MirMachine

tacazares / SeedMatchR

ETHZ-INS / scanMiR

jtremblay / MiRNATarget

lpantano / seqclusterViz

zavolanlab / mirflowz

ailab-seoultech / deepTarget

omics-datascience / modulector

YannDubs / miRNAseq-Analysis

zhangjunpeng411 / miRspongeR

Bohdan-Khomtchouk / Smalls

haichengyi / bioseq2vec

selcenari / ceRNAnetsim

zhangjunpeng411 / miRSM