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19 repositories

awesome-genomic-skills
Public
A curated list of awesome genomics and bioinformatics agentic skills, MCPs and benchmarks for Claude Code, Copilot, Codex, Cursor, Gemini CLI, etc
Creative Commons Zero v1.0 Universal
•6•35•0•1•Updated May 29, 2026May 29, 2026
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
•27•245•61•3•Updated May 20, 2026May 20, 2026
awesome-nanopore
Public
A curated list of awesome nanopore analysis tools.
machine-learning bioinformatics nanopore
machine-learning bioinformatics nanopore awesome-list
MIT License
•58•313•0•0•Updated May 20, 2026May 20, 2026
bambu-pipe
Public
Transcript discovery and quantification for long read single cell and spatial transcriptomics data using Bambu
rna-seq nanopore pipeline
rna-seq nanopore pipeline genomics nextflow pacbio transcriptomics single-cell transcript-quantification bambu
Nextflow
•
GNU General Public License v3.0
•1•22•9•0•Updated May 20, 2026May 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•161•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•59•12•0•Updated Jul 14, 2025Jul 14, 2025
m6anet
Public
Detection of m6A from direct RNA-Seq data
Python
•
MIT License
•21•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•165•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
•265•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•290•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
•1.1k•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

19 repositories

awesome-genomic-skills

bambu

awesome-nanopore

bambu-pipe

xpore-minimal-nextflow-pipeline

rnome-minimal-nextflow-pipeline

sg-nex-data

proActiv

m6anet

xpore

NanoporeRNASeq

nanoseq

containers

bioinformatics-workflows

ICGC_alternative_promoters

modules

proactivWorkflow

ncNAT_promoter_switch_code

nanorna-bam

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Repositories list

19 repositories