All

18 repositories

bambu
Public
Reference-guided transcript discovery and quantification for long read RNA-Seq data
rna-seq r nanopore
rna-seq r nanopore bioconductor transcriptomics rna-seq-analysis transcript-quantification bambu long-reads nanopore-sequencing
R
•
GNU General Public License v3.0
•28•238•63•5•Updated Apr 23, 2026Apr 23, 2026
bambu-singlecell-spatial
Public
Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu
Nextflow
•
GNU General Public License v3.0
•1•18•9•1•Updated Apr 20, 2026Apr 20, 2026
xpore-minimal-nextflow-pipeline
Public
A minimal nextflow pipeline to align (fastq) reads using minimap2, align raw nanopore signal (pod5) using f5c, and perform differential modification analysis us…
Nextflow
•
MIT License
•0•0•0•0•Updated Apr 6, 2026Apr 6, 2026
rnome-minimal-nextflow-pipeline
Public
Nextflow pipeline used for aligning nanopore modBAM files using minimap2 (preserving modification tags) and summarising modifications using modkit. Used to proc…
Nextflow
•
MIT License
•0•0•0•0•Updated Feb 26, 2026Feb 26, 2026
sg-nex-data
Public
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
rna-seq nanopore transcriptomics
rna-seq nanopore transcriptomics long-reads direct-rna-sequencing
R
•27•156•11•0•Updated Jan 23, 2026Jan 23, 2026
proActiv
Public
Estimation of Promoter Activity from RNA-Seq data
r genomics promoter-activity
r genomics promoter-activity rna-seq-data promoter-annotation alternative-promoters
R
•
Other
•16•57•12•0•Updated Jul 14, 2025Jul 14, 2025
awesome-nanopore
Public
A curated list of awesome nanopore analysis tools.
machine-learning bioinformatics nanopore
machine-learning bioinformatics nanopore awesome-list
MIT License
•57•309•1•1•Updated Jul 2, 2025Jul 2, 2025
m6anet
Public
Detection of m6A from direct RNA-Seq data
Python
•
MIT License
•20•131•25•0•Updated May 19, 2025May 19, 2025
xpore
Public
Identification of differential RNA modifications from nanopore direct RNA sequencing
python machine-learning rna-seq
python machine-learning rna-seq nanopore genomics rna transcriptomics modification nanopore-sequencing rna-modifications
Python
•
MIT License
•24•164•32•1•Updated Nov 7, 2024Nov 7, 2024
NanoporeRNASeq
Public
Nanopore RNASeq data
rna-seq r nanopore
rna-seq r nanopore bioconductor long-reads sg-nex
R
•
MIT License
•2•8•0•0•Updated Oct 25, 2022Oct 25, 2022
nanoseq
Public
Nanopore demultiplexing, QC and alignment pipeline
Nextflow
•
MIT License
•105•4•0•0•Updated Dec 17, 2021Dec 17, 2021
containers
Public
Bioinformatics containers
Dockerfile
•
Apache License 2.0
•266•3•0•0•Updated Nov 3, 2021Nov 3, 2021
bioinformatics-workflows
Public
minimal example implementations for bioinformatics workflow managers
workflow bioinformatics rna-seq
workflow bioinformatics rna-seq pipeline workflow-management bioinformatics-workflows
Python
•
MIT License
•50•285•2•1•Updated Oct 27, 2021Oct 27, 2021
ICGC_alternative_promoters
Public
A pipeline for alternative promoter analysis.
Nextflow
•
MIT License
•0•1•0•0•Updated May 27, 2021May 27, 2021
modules
Public
Repository to host tool-specific module files for the Nextflow DSL2 community!
Nextflow
•
MIT License
•1k•0•0•0•Updated May 5, 2021May 5, 2021
proactivWorkflow
Public
proActiv workflow: Identifying active and alternative promoters from RNA-Seq data
1•0•0•0•Updated Apr 22, 2021Apr 22, 2021
ncNAT_promoter_switch_code
Public
R
•0•0•0•0•Updated Aug 12, 2020Aug 12, 2020
nanorna-bam
Public
Downstream analysis of Nanopore RNA data - transcriptome reconstruction and feature counts (under development)
Nextflow
•
MIT License
•2•0•0•0•Updated Jul 2, 2020Jul 2, 2020

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Göke Lab

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All

18 repositories

bambu

bambu-singlecell-spatial

xpore-minimal-nextflow-pipeline

rnome-minimal-nextflow-pipeline

sg-nex-data

proActiv

awesome-nanopore

m6anet

xpore

NanoporeRNASeq

nanoseq

containers

bioinformatics-workflows

ICGC_alternative_promoters

modules

proactivWorkflow

ncNAT_promoter_switch_code

nanorna-bam

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Repositories list

18 repositories