Göke Lab

All

16 repositories

bambu
Public
Reference-guided transcript discovery and quantification for long read RNA-Seq data
r nanopore bioconductor transcriptomics rna-seq-analysis transcript-quantification bambu long-reads nanopore-sequencing transcript-reconstruction
R
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GNU General Public License v3.0
•25•212•52•5•Updated Jul 23, 2025Jul 23, 2025
proActiv
Public
Estimation of Promoter Activity from RNA-Seq data
r genomics promoter-activity rna-seq-data promoter-annotation alternative-promoters
R
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Other
•15•53•12•0•Updated Jul 14, 2025Jul 14, 2025
sg-nex-data
Public
Nanopore RNA-Seq data from the Singapore Nanopore-Expression Project
rna-seq transcriptomics long-reads direct-rna-sequencing nanopore
R
•25•129•10•0•Updated Jul 3, 2025Jul 3, 2025
awesome-nanopore
Public
A curated list of awesome nanopore analysis tools.
machine-learning nanopore awesome-list bioinformatics
MIT License
•51•283•1•0•Updated Jul 2, 2025Jul 2, 2025
bambu-singlecell-spatial
Public
Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu
Nextflow
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GNU General Public License v3.0
•1•14•4•2•Updated Jun 23, 2025Jun 23, 2025
m6anet
Public
Detection of m6A from direct RNA-Seq data
Python
•
MIT License
•19•125•21•0•Updated May 19, 2025May 19, 2025
xpore
Public
Identification of differential RNA modifications from nanopore direct RNA sequencing
machine-learning rna-seq nanopore genomics rna transcriptomics modification nanopore-sequencing rna-modifications python
Python
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MIT License
•23•153•31•1•Updated Nov 7, 2024Nov 7, 2024
NanoporeRNASeq
Public
Nanopore RNASeq data
rna-seq r nanopore bioconductor long-reads sg-nex
R
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MIT License
•2•8•0•0•Updated Oct 25, 2022Oct 25, 2022
nanoseq
Public
Nanopore demultiplexing, QC and alignment pipeline
Nextflow
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MIT License
•99•4•0•0•Updated Dec 17, 2021Dec 17, 2021
containers
Public
Bioinformatics containers
Dockerfile
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Apache License 2.0
•254•3•0•0•Updated Nov 3, 2021Nov 3, 2021
bioinformatics-workflows
Public
minimal example implementations for bioinformatics workflow managers
workflow-management bioinformatics-workflows workflow bioinformatics rna-seq pipeline
Python
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MIT License
•47•277•2•1•Updated Oct 27, 2021Oct 27, 2021
ICGC_alternative_promoters
Public
A pipeline for alternative promoter analysis.
Nextflow
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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
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MIT License
•883•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
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MIT License
•2•0•0•0•Updated Jul 2, 2020Jul 2, 2020