rna

There are 5 repositories under rna topic.

graphein
a-r-j / graphein
Protein Graph Library
protein protein-structure deep-learning pytorch graph-neural-networks dgl computational-biology bioinformatics structural-biology protein-data-bank protein-design geometric-deep-learning pytorch-geometric python interactomics interactome rna ppi-networks gene-regulatory-networks drug-discovery
Language:Jupyter Notebook 975
nf-core / rnaseq
RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.
nextflow nf-core pipeline rna rna-seq workflow
Language:Nextflow 770
seqviz
Lattice-Automation / seqviz
a JavaScript DNA, RNA, and protein sequence viewer
dna igem synthetic-biology vector plasmid rna biology protein
Language:TypeScript 211
tseemann / barrnap
:microscope: :leo: Bacterial ribosomal RNA predictor
rna hmmer rnammer hmm-model rrna annotations ribosomal
Language:Perl 202
nextstrain / nextclade
Viral genome alignment, mutation calling, clade assignment, quality checks and phylogenetic placement
clade clades coronavirus covid covid-19 dna ncov neherlab nextstrain research rna sars-cov-2 science sequences sequencing strain virus covid19 next-generation-sequencing influenza
Language:TypeScript 197
IsoSeq
PacificBiosciences / IsoSeq
Iso-Seq - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads
clustering discovery isoforms pacbio polishing rna
178
fjossinet / RNArtist
With RNArtist, you construct a collection of RNA structures that can be gathered into RNA families, projects,...
bioinformatics java javafx-application kotlin rna rna-secondary-structure rna-structure
Language:Kotlin 152
rna-tools
mmagnus / rna-tools
🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) used by RNA CASP, RNA PUZZLES, and me ;-) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online
rna-puzzle rna-pdb pdb rna rna-structure rosetta simrna bioinformatics python rna-tools
Language:Jupyter Notebook 136
nf-core / rnafusion
RNA-seq analysis pipeline for detection of gene-fusions
nf-core nextflow workflow rna-seq rna pipeline fusion-genes fusion gene-fusion
Language:Nextflow 128
xpore
GoekeLab / xpore
Identification of differential RNA modifications from nanopore direct RNA sequencing
rna modification transcriptomics machine-learning genomics nanopore-sequencing rna-seq rna-modifications nanopore python
Language:Python 127
bgruening / galaxytools
:microscope::books: Galaxy Tool wrappers
galaxyproj galaxy wrapper rna cheminformatics tools hacktoberfest
Language:HTML 113
ga4gh / ga4gh-server
Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24
ga4gh genomics server global alliance health variants rna genome-annotation reference-implementation bioinformatics python
Language:Python 97
jaswindersingh2 / SPOT-RNA
RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.
rna rna-secondary-structure deep-learning transfer-learning ensemble-model resnet blstm-neural-networks tensorflow rna-secondary-structure-prediction canonical-base-pairs noncanonical-base-pairs pseudoknot-base-pairs pdb-dataset bprna-dataset multiplets-base-pairs lone-pairs machine-learning rna-structure rna-structural-analysis rna-structure-motifs
Language:Perl 91
mozack / abra2
ABRA2
splice-junctions indels dna rna realigner ngs abra
Language:Java 88
Lattice-Automation / seqfold
nucleic acid folding
dna rna folding rna-structure-prediction dna-structure-prediction structure-prediction rna-folding dna-folding
Language:Python 74
R2DT
RNAcentral / R2DT
Visualise RNA secondary structure in consistent, reproducible and recognisable layouts
rna bioinformatics python3 rna-secondary-structure visualisation
Language:PostScript 57
nf-core / hlatyping
Precision HLA typing from next-generation sequencing data
dna hla hla-typing immunology nextflow nf-core optitype personalized-medicine pipeline rna workflow
Language:Nextflow 50
KirillKryukov / naf
Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences
compression dna fasta fastq file-format protein rna
Language:C 49
adnaniazi / tailfindr
An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.
bioinformatics cdna nanopore r rna
Language:R 47
1ytic / warp-rna
Recurrent Neural Aligner
rna rnn-transducer forward-backward cuda
Language:Python 46
BackofenLab / IntaRNA
Efficient target prediction incorporating accessibility of interaction sites
bioinformatics interaction rna structure tool
Language:C++ 44
bgruening / galaxy-rna-workbench
Galaxy RNA workbench
galaxy galaxy-docker rna sequencing science galaxyproject
Language:HTML 37
UMCUGenetics / RNASeq
RNASeq pipeline
sequencing read-counts rna rna-seq pipeline
Language:Perl 35
yikunpku / RNA-MSM
RNA-MSM model is an unsupervised RNA language model based on multiple sequences that outputs both embedding and attention map to match different types of downstream tasks.
bioinformatics language-model rna
Language:Python 35
BackofenLab / RNA-Playground
Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.
rna bioinformatics nussinov teaching alignment structure-prediction algorithm
Language:JavaScript 34
srnas / barnaba
Analyse Nucleic Acids Structure and Simulations with baRNAba
rna-structure python molecular-dynamics modeling rna rna-folding
Language:Jupyter Notebook 34
nf-core / rnasplice
rnasplice is a bioinformatics pipeline for RNA-seq alternative splicing analysis
alternative-splicing nextflow nf-core pipeline rna rna-seq splicing workflow
Language:Nextflow 32
nf-core / lncpipe
UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets
lncrna rna-seq-analysis transcriptome differential-expression nf-core nextflow workflow pipeline rna long-non-coding non-coding
Language:Nextflow 30
nf-core / rnavar
gatk4 RNA variant calling pipeline
gatk4 variant-calling rnaseq rna worflow pipeline nextflow nf-core workflow
Language:Nextflow 28
RNAcentral / rnacentral-webcode
RNAcentral website source code
rna bioinformatics biology ncrna python django django-rest-framework docker postgres database kubernetes
Language:Python 28
fjossinet / RNArtistCore
A Kotlin DSL to create and plot RNA 2D structures. The drawing engine behind RNArtist to be used from the command line.
bioinformatics drawing-algorithm dsl java kotlin plot-rna rna rna-molecule rna-secondary-structure rna-structure visualization
Language:Kotlin 26
nanoporetech / pipeline-nanopore-denovo-isoforms
Pipeline for de novo clustering of long transcriptomic reads
cdna rna rna-seq transcriptomics
Language:Python 26
fjossinet / RNA-Science-Toolbox
A platform to do RNA science
bioinformatics python rna rna-structure
Language:Jupyter Notebook 25
comprna / CHEUI
Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing
deep-neural-networks epitranscriptomics nanopore rna deep-learning rna-methylation
Language:C++ 24
fingeRNAt
n-szulc / fingeRNAt
Software for detecting non-covalent interactions formed within complexes of nucleic acids with ligands.
nucleic-acids bioinformatics-tool structural-bioinformatics rna-ligand-complexes ligand-receptor-interaction drug-target-interactions ligand-target bioinformatics scientific-computing ligand-complex structural-interaction-fingerprint rna dna interactions molecular-interactions
Language:Python 24
nf-core / isoseq
Genome annotation with PacBio Iso-Seq. Takes raw subreads as input, generate Full Length Non Chemiric (FLNC) sequences and produce a bed annotation.
isoseq isoseq-3 nextflow nf-core pipeline rna tama ultra workflow
Language:Nextflow 23