mirna

There are 1 repository 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 130
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 45
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 40
lpantano / seqcluster
small RNA analysis from NGS data
smallrna mirna trna report sequencing
Language:HTML 35
biocoder / Perl-for-Bioinformatics
An attempt to help anyone interested in using Perl for Bioinformatics
bioinformatics pipeline perl ncrna lncrna mirna
Language:Python 32
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.
bioinformatics bioinformatics-pipeline biomarker-discovery biomarkers classification data-mining data-science deep-learning deep-neural-networks docker-image feature-selection mirna neural-network next-generation-sequencing omics qpcr r r-package rna-seq variable-selection
Language:R 31
dmnfarrell / smallrnaseq
small rna-seq analysis package
bioinformatics genomics mirna python rna-seq sequencing smallrna
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:Jupyter Notebook 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 13
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 mirna-identification mirna-secondary-structure pre-mirna pytorch
Language:Python 11
kevinniechen / quagmir
isomiR quantification and analysis pipeline
cancer-genomics-cloud mirna pipeline sequencing
Language:Python 9
lpantano / isomiRs
analyze isomiRs from seqbuster tool
analyze-isomirs bioconductor isomirs mirna r
Language:R 8
TBradley27 / FilTar
Using RNA-Seq data to improve microRNA target prediction accuracy in animals
mirna-targets mirna mirna-mrna-interaction
Language:Python 8
NACHO
mcanouil / NACHO
NAnostring quality Control dasHbOard
nanostring shiny quality-control normalisation r-package r-stats rstats mirna mrna
Language:R 7
saorisakaue / MIGWAS
A software to detect genome-wide miRNA-gene enrichment signal.
mirna bioinformatics
Language:Python 7
HCGB-IGTP / XICRA
Small RNAseq pipeline for paired-end reads
pipeline mirna smallrna-seq python
Language:Python 6
lpantano / seqclusterViz
visualization of seqcluster output, try at:
mirna smallrna smallrna-seq trna-derived-small-rna visualization
Language:JavaScript 6
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 6
sing-group / my-brain-seq
myBrain-Seq: a Compi pipeline for miRNA-Seq data analysis in neuropsychiatry
differential-expression docker mirna mirna-seq compi pipeline
Language:R 6
ailab-seoultech / deepTarget
microrna mirna deep-learning convolutional-neural-networks cnns
Language:Python 5
scanMiR
ETHZ-INS / scanMiR
A set of tools for scanning for miRNA binding sites and working with affinity models
mirna scanning tdmd
Language:R 5
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 5
tacazares / SeedMatchR
Off-target analysis of siRNA knock down paired with RNAseq
deseq2-analysis mirna rna-seq sirna transcriptomics
Language:R 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
zavolanlab / mirflowz
Snakemake workflow for the mapping and quantification of miRNAs and isomiRs from miRNA-Seq libraries.
bioinformatics isomirs mirna snakemake workflow
Language:Python 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
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 4
selcenari / ceRNAnetsim
Simulation of interactions miRNA:Competing Targets
r network-simulator tidygraph tidyverse network-biology mirna tcga cerna
Language:R 4
sinanugur / MirMachine
MirMachine, a command line tool to detect microRNA homologs in genome sequences.
bioinformatics mirna prediction covariance-model
Language:Python 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
msls-bioinfo / CmiRClustFinder_v1.0
CmiRClustFinder v1.0: a tool for identification of CNV co-locolized miRNA, miRNA clusers and genes in TCGA cancer cohorts.
mirna cnv tcga
Language:R 3
zhangjunpeng411 / Scan
Scanning sample-specific miRNA regulation from bulk and single-cell RNA-sequencing data
gene-regulation mirna mirna-targets single-cell-analysis single-cell-rna-seq
Language:HTML 3

mirna

rajewsky-lab / mirdeep2

junchaoshi / sports1.1

nf-core / circrna

lpantano / seqcluster

biocoder / Perl-for-Bioinformatics

kstawiski / OmicSelector

dmnfarrell / smallrnaseq

gitHBDX / TransfoRNA

miRTop / mirtop

eandresleon / miARma-seq

zhangjunpeng411 / LncmiRSRN

peace195 / miRNA-identification-conv2D

kevinniechen / quagmir

lpantano / isomiRs

TBradley27 / FilTar

mcanouil / NACHO

saorisakaue / MIGWAS

HCGB-IGTP / XICRA

lpantano / seqclusterViz

omics-datascience / modulector

sing-group / my-brain-seq

ailab-seoultech / deepTarget

ETHZ-INS / scanMiR

jtremblay / MiRNATarget

tacazares / SeedMatchR

YannDubs / miRNAseq-Analysis

zavolanlab / mirflowz

zhangjunpeng411 / miRspongeR

Bohdan-Khomtchouk / Smalls

haichengyi / bioseq2vec

multitalk / miRTalk

selcenari / ceRNAnetsim

sinanugur / MirMachine

zhangjunpeng411 / miRSM

msls-bioinfo / CmiRClustFinder_v1.0

zhangjunpeng411 / Scan