#

rna

Here are 297 public repositories matching this topic...

nf-core / rnaseq

RNA sequencing analysis pipeline using STAR, RSEM, HISAT2 or Salmon with gene/isoform counts and extensive quality control.

workflow rna-seq pipeline nextflow rna nf-core

Updated May 17, 2022
Nextflow

graphein

a-r-j / graphein

Sponsor

Open

Add additional inputs for CLI

a-r-j commented Mar 8, 2022

Describe the solution you'd like

inputs for chain selection as a separate .txt file
Input as list of PDB codes (txt file) rather than PDB directory path

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enhancement good first issue

Open

YAML Configs for existing methods

Open

Add distances as edge features

nextstrain / nextclade

Open

docs: broken image links on QC page

1

victorlin commented Apr 28, 2022

Example: https://docs.nextstrain.org/projects/nextclade/en/stable/user/algorithm/07-quality-control.html

https://github.com/nextstrain/nextclade/blob/ccf2a0429e239e29a20dd4da1148b908ed2d8515/docs/user/algorithm/07-quality-control.md?plain=1#L51

gets rendered as:

<img alt="Identification of private mutations" src="/docs/user/assets/algo_private-muts.png">

and the absolute

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t:bug good first issue help wanted

Open

ENH: Surface insertions in mutation view

3

Open

flag to print shortenered list of dataset

1

Find more good first issues

tseemann / barrnap

🔬

♌ Bacterial ribosomal RNA predictor

annotations rna hmm-model hmmer rnammer rrna ribosomal

Updated Jan 2, 2021
Perl

IsoSeq

PacificBiosciences / IsoSeq

IsoSeq3 - Scalable De Novo Isoform Discovery from Single-Molecule PacBio Reads

clustering discovery pacbio rna isoforms polishing

Updated May 19, 2022

bgruening / galaxytools

🔬

📚 Galaxy Tool wrappers

wrapper tools cheminformatics rna galaxy hacktoberfest galaxyproj

Updated May 18, 2022
HTML

ga4gh / ga4gh-server

Reference implementation of the APIs defined in ga4gh-schemas. RETIRED 2018-01-24

python bioinformatics server genomics health variants global rna genome-annotation ga4gh reference-implementation alliance

Updated Jan 24, 2018
Python

xpore

GoekeLab / xpore

Identification of differential RNA modifications from nanopore direct RNA sequencing

machine-learning rna-seq genomics rna transcriptomics modification nanopore-sequencing rna-modifications

Updated Feb 10, 2022
Python

rna-tools

mmagnus / rna-tools

🔧rna-tools: a toolbox to analyze sequences, structures and simulations of RNA (and more) docs @ http://rna-tools.rtfd.io web @ http://rna-tools.online

python bioinformatics pdb rna-structure rna rna-puzzle rna-pdb rosetta simrna

Updated May 19, 2022
Jupyter Notebook

mozack / abra2

ABRA2

ngs dna rna indels abra splice-junctions realigner

Updated Oct 11, 2021
Java

nf-core / rnafusion

RNA-seq analysis pipeline for detection gene-fusions

workflow rna-seq pipeline nextflow gene-fusion fusion rna fusion-genes nf-core

Updated May 19, 2022
Nextflow

fjossinet / RNArtist

RNArtist allows you to design and paint your RNA 2D structures interactively. Coupled with the 3D viewer UCSF Chimera, use your 2D as a map to explore RNA 3D architectures.

kotlin java bioinformatics rna-structure rna javafx-application rna-secondary-structure

Updated Mar 11, 2022
Kotlin

jaswindersingh2 / SPOT-RNA

RNA Secondary Structure Prediction using an Ensemble of Two-dimensional Deep Neural Networks and Transfer Learning.

machine-learning deep-learning tensorflow rna-structure rna resnet transfer-learning ensemble-model rna-structural-analysis blstm-neural-networks rna-secondary-structure rna-secondary-structure-prediction canonical-base-pairs noncanonical-base-pairs pseudoknot-base-pairs pdb-dataset bprna-dataset multiplets-base-pairs lone-pairs rna-structure-motifs

Updated Mar 21, 2022
Perl

1ytic / warp-rna

Recurrent Neural Aligner

cuda rna forward-backward rnn-transducer

Updated Apr 14, 2020
Python

bgruening / galaxy-rna-workbench

Galaxy RNA workbench

science sequencing rna galaxy galaxyproject galaxy-docker

Updated Oct 10, 2020
HTML

Lattice-Automation / seqfold

minimalistic nucleic acid folding

dna rna folding rna-structure-prediction structure-prediction nucleic-acids energy-functions dna-structure-prediction

Updated Mar 27, 2022
Python

KirillKryukov / naf

Nucleotide Archival Format - Compressed file format for DNA/RNA/protein sequences

compression dna file-format protein rna fasta fastq

Updated Mar 3, 2022
C

BackofenLab / IntaRNA

Efficient target prediction incorporating accessibility of interaction sites

bioinformatics tool structure rna interaction

Updated May 5, 2022
C++

R2DT

RNAcentral / R2DT

Open

Make it easier to update Traveler

AntonPetrov commented Sep 29, 2021

We need to develop an easier way to update Traveler in R2DT. Currently there is a set of test sequences and their corresponding diagrams. The tests only pass if all newly generated diagrams are identical to the examples, which gives confidence that no accidental changes

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enhancement good first issue

UMCUGenetics / RNASeq

RNASeq pipeline

rna-seq pipeline sequencing rna read-counts

Updated Oct 28, 2019
Perl

nf-core / hlatyping

Precision HLA typing from next-generation sequencing data

workflow pipeline nextflow dna rna immunology hla optitype hla-typing personalized-medicine nf-core

Updated May 16, 2022
Nextflow

adnaniazi / tailfindr

An R package for estimating poly(A)-tail lengths in Oxford Nanopore RNA and DNA reads.

bioinformatics r nanopore rna cdna

Updated Mar 30, 2022
R

nf-core / lncpipe

UNDER DEVELOPMENT--- Analysis of long non-coding RNAs from RNA-seq datasets

workflow pipeline nextflow rna transcriptome rna-seq-analysis differential-expression lncrna non-coding nf-core long-non-coding

Updated May 16, 2022
Nextflow

RNAcentral / rnacentral-webcode

RNAcentral website source code

css python docker kubernetes twitter-bootstrap postgres django bioinformatics database biology feedback django-rest-framework rna ncrna rnacentral

Updated May 20, 2022
Python

srnas / barnaba

Analyse Nucleic Acids Structure and Simulations with baRNAba

python modeling molecular-dynamics rna-structure rna rna-folding

Updated Jan 19, 2022
Jupyter Notebook

BackofenLab / RNA-Playground

Visualize the inner workings of RNA bioinformatics algorithms for structure prediction, interaction prediction and sequence alignment.

bioinformatics algorithm teaching alignment rna nussinov structure-prediction

Updated Nov 11, 2021
JavaScript

fjossinet / RNArtistCore

A Kotlin DSL and library to create and plot RNA 2D structures

visualization kotlin java bioinformatics dsl rna-structure rna drawing-algorithm rna-secondary-structure rna-molecule plot-rna

Updated Feb 23, 2022
Kotlin

fjossinet / RNA-Science-Toolbox

A platform to do RNA science

python bioinformatics rna-structure rna

Updated Mar 7, 2021
Jupyter Notebook

drivenbyentropy / aptasuite

A full-featured bioinformatics software collection for the comprehensive analysis of aptamers in HT-SELEX experiments.

java gui bioinformatics deep-learning analysis clustering computational-biology dna rna graphical-user-interface ht-selex sequence-structure-motif aptasim aptatrace aptamers in-vitro-selection aptacluster aptasuite selex ht-selex-experiments

Updated May 4, 2022
Java

nanoporetech / pipeline-nanopore-denovo-isoforms

Pipeline for de novo clustering of long transcriptomic reads

rna-seq rna transcriptomics cdna

Updated Jan 26, 2022
Python

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