Computational RNA Biology group

All

33 repositories

dFORCE
Public
Jupyter Notebook
•0•0•0•0•Updated Jun 17, 2025Jun 17, 2025
SWARM
Public
Single-molecule Workflow for Analysing RNA Modifications
C++
•1•4•0•0•Updated May 28, 2025May 28, 2025
R2Dtool
Public
Analyse RNA feature distributions.
rna-seq nanopore long-read transcriptomics epitranscriptomics
Jupyter Notebook
•
MIT License
•4•16•3•0•Updated Dec 16, 2024Dec 16, 2024
riser
Public
Biochemical-free enrichment or depletion of RNA classes in real-time during direct RNA sequencing
deep-learning nanopore rna
Python
•
GNU General Public License v3.0
•4•15•1•0•Updated Oct 2, 2024Oct 2, 2024
CHEUI
Public
Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing
deep-neural-networks deep-learning nanopore rna epitranscriptomics rna-methylation
C++
•
Other
•3•40•3•0•Updated Jul 19, 2024Jul 19, 2024
SVM-BPfinder-3M
Public
Python
•
GNU General Public License v3.0
•0•1•0•0•Updated Jul 2, 2024Jul 2, 2024
SVM-BPfinder
Public
Python
•
GNU General Public License v3.0
•1•1•0•0•Updated Jul 2, 2024Jul 2, 2024
SUPPA
Public
SUPPA: Fast quantification of splicing and differential splicing
splicing-quantification differential-splicing-analysis psi-calculation transcript-isoform psi-values clustered-events inclusion-level
Python
•
MIT License
•64•277•52•1•Updated Jun 19, 2024Jun 19, 2024
RATTLE
Public
Reference-free reconstruction and error correction of transcriptomes from Nanopore long-read sequencing
bioinformatics rna-seq genomics nanopore clustering transcriptome
C++
•
GNU General Public License v3.0
•10•57•24•0•Updated Feb 15, 2024Feb 15, 2024
METEORE
Public
Automatic DNA methylation detection from nanopore tools and their consensus model
R
•
MIT License
•18•79•6•1•Updated May 22, 2023May 22, 2023
ISOTOPE
Public
ISOform-guided prediction of epiTOPEs in cancer
alternative-splicing epitopes-prediction cancer
Python
•
GNU General Public License v3.0
•6•14•3•0•Updated Apr 10, 2023Apr 10, 2023
reorientexpress
Public
Transcriptome long-read orientation with Deep Learning
machine-learning deep-learning convolutional-neural-networks multilayer-perceptron-network nanopore-sequencing long-read-sequencing
Python
•
MIT License
•4•9•2•1•Updated Mar 25, 2023Mar 25, 2023
CHEUI-public
Public
Concurrent identification of m6A and m5C modifications in individual molecules from nanopore sequencing
deep-neural-networks deep-learning nanopore rna epitranscriptomics rna-methylation
Other
•0•1•0•0•Updated Nov 13, 2022Nov 13, 2022
radian
Public
Nanopore direct RNA basecaller
deep-learning nanopore rna language-model basecalling
Python
•
GNU General Public License v3.0
•2•11•0•1•Updated Oct 27, 2022Oct 27, 2022
txannotate
Public
MIT License
•0•0•0•0•Updated Sep 2, 2022Sep 2, 2022
drug_screening
Public
R
•
GNU General Public License v3.0
•0•0•0•0•Updated May 24, 2022May 24, 2022
risk_model_app
Public
Shiny App to predict a risk score for infant B-ALL patients
R
•
GNU General Public License v3.0
•0•0•0•0•Updated May 13, 2022May 13, 2022
ISOTOPE_supplementary
Public
Supplementary repository for file storage
0•0•0•0•Updated Jul 26, 2021Jul 26, 2021
ORQAS
Public
ORF Quantification pipeline for Alternative Splicing
translation differential-splicing-analysis quantification ribo-seq
Python
•
GNU General Public License v3.0
•6•16•2•0•Updated May 11, 2021May 11, 2021
CREOLE
Public
Reference-free identification of open reading frames and encoded proteins from nanopore transcriptomic long reads
Python
•1•2•0•0•Updated Jan 18, 2021Jan 18, 2021
Junckey
Public
Collection of scripts for computing PSI of junction clusters
splicing aberrant-splicing read-junctions junctions-clusters
Python
•3•7•1•0•Updated Oct 14, 2020Oct 14, 2020
MoSEA
Public
Motif Scan and Enrichment Analysis (MoSEA)
motif-enrichment-analysis
Python
•
ISC License
•9•16•6•0•Updated Oct 6, 2020Oct 6, 2020
ePydoor
Public
Epitope discovery pipeline for RNA-seq
cancer splicing-derived-neoepitopes epitope-discovery
Python
•1•6•0•0•Updated Dec 3, 2019Dec 3, 2019
calindel
Public
tool to calculate substitutions, indels etc
Python
•1•0•0•0•Updated Nov 26, 2019Nov 26, 2019
FLIPPER
Public
Read orientation and full transcript detection from Nanopore cDNA/RNA sequencing
C++
•
GNU General Public License v3.0
•1•1•0•0•Updated Aug 29, 2018Aug 29, 2018
MIRA
Public
Mutation Identification for RNA Alterations
Python
•2•6•0•0•Updated Jul 3, 2018Jul 3, 2018
humming
Public
Tools for the comparison of long-read mappings to a genome reference and annotations
Perl
•
MIT License
•2•2•0•0•Updated Apr 7, 2018Apr 7, 2018
SUPPA_supplementary_data
Public
Supplementary data
R
•7•5•2•0•Updated Feb 13, 2018Feb 13, 2018
Splicing_Browser
Public
Browser to present splicing events and junctions arround the genome
R
•1•2•0•0•Updated Nov 30, 2017Nov 30, 2017
LatentEvents
Public
Latent Dirichlet Allocation on alternative splicing events.
Python
•1•5•0•0•Updated Aug 14, 2017Aug 14, 2017