René's URL Explorer Experiment

Title: GitHub - GoekeLab/bambu: Reference-guided transcript discovery and quantification for long read RNA-Seq data · GitHub

Open Graph Title: GitHub - GoekeLab/bambu: Reference-guided transcript discovery and quantification for long read RNA-Seq data

X Title: GitHub - GoekeLab/bambu: Reference-guided transcript discovery and quantification for long read RNA-Seq data

Description: Reference-guided transcript discovery and quantification for long read RNA-Seq data - GitHub - GoekeLab/bambu: Reference-guided transcript discovery and quantification for long read RNA-Seq data

Open Graph Description: Reference-guided transcript discovery and quantification for long read RNA-Seq data - GoekeLab/bambu

X Description: Reference-guided transcript discovery and quantification for long read RNA-Seq data - GoekeLab/bambu

Opengraph URL: https://github.com/GoekeLab/bambu

X: @github

direct link

Domain: github.com

route-pattern	/:user_id/:repository
route-controller	files
route-action	disambiguate
fetch-nonce	v2:dfca398d-8888-546e-7b44-56bd91285a61
current-catalog-service-hash	f3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id	84FE:17F796:2A5CE4:38D237:6A4C6F36
html-safe-nonce	1eb28479f0eb36f932b1a06a5c1517940941348c14f487cf6d70547dff4f7436
visitor-payload	eyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI4NEZFOjE3Rjc5NjoyQTVDRTQ6MzhEMjM3OjZBNEM2RjM2IiwidmlzaXRvcl9pZCI6Ijc3NTE4NzkzNDA2Njk1NjI2NzgiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmac	311dbeea39d59ee1d4242afb12c9c256a98b407ea33c084032cb45bd700af356
hovercard-subject-tag	repository:238860759
github-keyboard-shortcuts	repository,copilot
google-site-verification	Apib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-url	https://collector.github.com/github/collect
analytics-location	//
fb:app_id	1401488693436528
apple-itunes-app	app-id=1477376905, app-argument=https://github.com/GoekeLab/bambu
twitter:image	https://repository-images.githubusercontent.com/238860759/bd7e5c80-b4a5-11ea-9da0-7545335cace8
twitter:card	summary_large_image
og:image	https://repository-images.githubusercontent.com/238860759/bd7e5c80-b4a5-11ea-9da0-7545335cace8
og:image:alt	Reference-guided transcript discovery and quantification for long read RNA-Seq data - GoekeLab/bambu
og:site_name	GitHub
og:type	object
hostname	github.com
expected-hostname	github.com
None	3d11bb817438277de2a940854450e83a7d32b6aeb5014e9e6b00a6423900251c
turbo-cache-control	no-cache
go-import	github.com/GoekeLab/bambu git https://github.com/GoekeLab/bambu.git
octolytics-dimension-user_id	46366103
octolytics-dimension-user_login	GoekeLab
octolytics-dimension-repository_id	238860759
octolytics-dimension-repository_nwo	GoekeLab/bambu
octolytics-dimension-repository_public	true
octolytics-dimension-repository_is_fork	false
octolytics-dimension-repository_network_root_id	238860759
octolytics-dimension-repository_network_root_nwo	GoekeLab/bambu
turbo-body-classes	logged-out env-production page-responsive
disable-turbo	false
browser-stats-url	https://api.github.com/_private/browser/stats
browser-errors-url	https://api.github.com/_private/browser/errors
release	14099438da5379150f15a2892474c7c7e6c0e55e
ui-target	full
theme-color	#1e2327
color-scheme	light dark

Links:

Skip to content	https://github.com/GoekeLab/bambu#start-of-content
	https://github.com/
Sign in	https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2FGoekeLab%2Fbambu
GitHub CopilotWrite better code with AI	https://github.com/features/copilot
GitHub Copilot appDirect agents from issue to merge	https://github.com/features/ai/github-app
MCP RegistryNewIntegrate external tools	https://github.com/mcp
ActionsAutomate any workflow	https://github.com/features/actions
CodespacesInstant dev environments	https://github.com/features/codespaces
IssuesPlan and track work	https://github.com/features/issues
Code ReviewManage code changes	https://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilities	https://github.com/security/advanced-security
Code securitySecure your code as you build	https://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they start	https://github.com/security/advanced-security/secret-protection
Why GitHub	https://github.com/why-github
Documentation	https://docs.github.com
Blog	https://github.blog
Changelog	https://github.blog/changelog
Marketplace	https://github.com/marketplace
View all features	https://github.com/features
Enterprises	https://github.com/enterprise
Small and medium teams	https://github.com/team
Startups	https://github.com/enterprise/startups
Nonprofits	https://github.com/solutions/industry/nonprofits
App Modernization	https://github.com/solutions/use-case/app-modernization
DevSecOps	https://github.com/solutions/use-case/devsecops
DevOps	https://github.com/solutions/use-case/devops
CI/CD	https://github.com/solutions/use-case/ci-cd
View all use cases	https://github.com/solutions/use-case
Healthcare	https://github.com/solutions/industry/healthcare
Financial services	https://github.com/solutions/industry/financial-services
Manufacturing	https://github.com/solutions/industry/manufacturing
Government	https://github.com/solutions/industry/government
View all industries	https://github.com/solutions/industry
View all solutions	https://github.com/solutions
AI	https://github.com/resources/articles?topic=ai
Software Development	https://github.com/resources/articles?topic=software-development
DevOps	https://github.com/resources/articles?topic=devops
Security	https://github.com/resources/articles?topic=security
View all topics	https://github.com/resources/articles
Customer stories	https://github.com/customer-stories
Events & webinars	https://github.com/resources/events
Ebooks & reports	https://github.com/resources/whitepapers
Business insights	https://github.com/solutions/executive-insights
GitHub Skills	https://skills.github.com
Documentation	https://docs.github.com
Customer support	https://support.github.com
Community forum	https://github.com/orgs/community/discussions
Trust center	https://github.com/trust-center
Partners	https://github.com/partners
View all resources	https://github.com/resources
GitHub SponsorsFund open source developers	https://github.com/sponsors
Security Lab	https://securitylab.github.com
Maintainer Community	https://maintainers.github.com
Accelerator	https://github.com/accelerator
GitHub Stars	https://stars.github.com
Archive Program	https://archiveprogram.github.com
Topics	https://github.com/topics
Trending	https://github.com/trending
Collections	https://github.com/collections
Enterprise platformAI-powered developer platform	https://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security features	https://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI features	https://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 support	https://github.com/premium-support
Pricing	https://github.com/pricing
Search syntax tips	https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentation	https://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in	https://github.com/login?return_to=https%3A%2F%2Fgithub.com%2FGoekeLab%2Fbambu
Sign up	https://github.com/signup?ref_cta=Sign+up&ref_loc=header+logged+out&ref_page=%2F%3Cuser-name%3E%2F%3Crepo-name%3E&source=header-repo&source_repo=GoekeLab%2Fbambu
Reload	https://github.com/GoekeLab/bambu
Reload	https://github.com/GoekeLab/bambu
Reload	https://github.com/GoekeLab/bambu
Please reload this page	https://github.com/GoekeLab/bambu
GoekeLab	https://github.com/GoekeLab
bambu	https://github.com/GoekeLab/bambu
Notifications	https://github.com/login?return_to=%2FGoekeLab%2Fbambu
Fork 27	https://github.com/login?return_to=%2FGoekeLab%2Fbambu
Star 248	https://github.com/login?return_to=%2FGoekeLab%2Fbambu
Code	https://github.com/GoekeLab/bambu
Issues 53	https://github.com/GoekeLab/bambu/issues
Pull requests 1	https://github.com/GoekeLab/bambu/pulls
Discussions	https://github.com/GoekeLab/bambu/discussions
Actions	https://github.com/GoekeLab/bambu/actions
Projects	https://github.com/GoekeLab/bambu/projects
Security and quality 0	https://github.com/GoekeLab/bambu/security
Insights	https://github.com/GoekeLab/bambu/pulse
Code	https://github.com/GoekeLab/bambu
Issues	https://github.com/GoekeLab/bambu/issues
Pull requests	https://github.com/GoekeLab/bambu/pulls
Discussions	https://github.com/GoekeLab/bambu/discussions
Actions	https://github.com/GoekeLab/bambu/actions
Projects	https://github.com/GoekeLab/bambu/projects
Security and quality	https://github.com/GoekeLab/bambu/security
Insights	https://github.com/GoekeLab/bambu/pulse
	https://github.com/GoekeLab/bambu
Branches	https://github.com/GoekeLab/bambu/branches
Tags	https://github.com/GoekeLab/bambu/tags
	https://github.com/GoekeLab/bambu/branches
	https://github.com/GoekeLab/bambu/tags
2,455 Commits	https://github.com/GoekeLab/bambu/commits/devel/
	https://github.com/GoekeLab/bambu/commits/devel/
.github	https://github.com/GoekeLab/bambu/tree/devel/.github
.github	https://github.com/GoekeLab/bambu/tree/devel/.github
R	https://github.com/GoekeLab/bambu/tree/devel/R
R	https://github.com/GoekeLab/bambu/tree/devel/R
data-raw	https://github.com/GoekeLab/bambu/tree/devel/data-raw
data-raw	https://github.com/GoekeLab/bambu/tree/devel/data-raw
docs	https://github.com/GoekeLab/bambu/tree/devel/docs
docs	https://github.com/GoekeLab/bambu/tree/devel/docs
figures	https://github.com/GoekeLab/bambu/tree/devel/figures
figures	https://github.com/GoekeLab/bambu/tree/devel/figures
inst	https://github.com/GoekeLab/bambu/tree/devel/inst
inst	https://github.com/GoekeLab/bambu/tree/devel/inst
man	https://github.com/GoekeLab/bambu/tree/devel/man
man	https://github.com/GoekeLab/bambu/tree/devel/man
src	https://github.com/GoekeLab/bambu/tree/devel/src
src	https://github.com/GoekeLab/bambu/tree/devel/src
tests	https://github.com/GoekeLab/bambu/tree/devel/tests
tests	https://github.com/GoekeLab/bambu/tree/devel/tests
vignettes	https://github.com/GoekeLab/bambu/tree/devel/vignettes
vignettes	https://github.com/GoekeLab/bambu/tree/devel/vignettes
.Rbuildignore	https://github.com/GoekeLab/bambu/blob/devel/.Rbuildignore
.Rbuildignore	https://github.com/GoekeLab/bambu/blob/devel/.Rbuildignore
.gitignore	https://github.com/GoekeLab/bambu/blob/devel/.gitignore
.gitignore	https://github.com/GoekeLab/bambu/blob/devel/.gitignore
DESCRIPTION	https://github.com/GoekeLab/bambu/blob/devel/DESCRIPTION
DESCRIPTION	https://github.com/GoekeLab/bambu/blob/devel/DESCRIPTION
LICENSE	https://github.com/GoekeLab/bambu/blob/devel/LICENSE
LICENSE	https://github.com/GoekeLab/bambu/blob/devel/LICENSE
NAMESPACE	https://github.com/GoekeLab/bambu/blob/devel/NAMESPACE
NAMESPACE	https://github.com/GoekeLab/bambu/blob/devel/NAMESPACE
NEWS	https://github.com/GoekeLab/bambu/blob/devel/NEWS
NEWS	https://github.com/GoekeLab/bambu/blob/devel/NEWS
README.md	https://github.com/GoekeLab/bambu/blob/devel/README.md
README.md	https://github.com/GoekeLab/bambu/blob/devel/README.md
README	https://github.com/GoekeLab/bambu
GPL-3.0 license	https://github.com/GoekeLab/bambu
	https://github.com/GoekeLab/bambu/blob/devel/figures/transparent-bambu.png
	https://github.com/GoekeLab/bambu#bambu-context-aware-transcript-quantification-from-long-read-rna-seq-data
	https://www.tidyverse.org/lifecycle/#stable
	https://github.com/GoekeLab/bambu/graphs/contributors
	https://github.com/GoekeLab/bambu#installation
	https://github.com/goekelab/bambu/actions
	https://github.com/goekelab/bambu/issues
	https://github.com/goekelab/bambu/pulls
	http://bioconductor.org/checkResults/release/bioc-LATEST/bambu/
	https://bioconductor.org/checkResults/devel/bioc-LATEST/bambu
	https://www.gnu.org/licenses/gpl-3.0
	https://www.codefactor.io/repository/github/goekelab/bambu
	https://codecov.io/gh/GoekeLab/bambu
	https://github.com/GoekeLab/bambu#content
Installation	https://github.com/GoekeLab/bambu#installation
General Usage	https://github.com/GoekeLab/bambu#General-Usage
Using precalculated annotation objects	https://github.com/GoekeLab/bambu#Using-precalculated-annotation-objects
Running multiple samples	https://github.com/GoekeLab/bambu#Running-multiple-samples
Modulating the sensitivity of discovery (pre and post analysis)	https://github.com/GoekeLab/bambu#Modulating-the-sensitivity-of-discovery-pre-and-post-analysis
Output	https://github.com/GoekeLab/bambu#Output
Visualization	https://github.com/GoekeLab/bambu#Visualization
bambu Advanced Options	https://github.com/GoekeLab/bambu#Bambu-Advanced-Options
Using a pretrained model	https://github.com/GoekeLab/bambu#Using-a-pretrained-model
De-novo transcript discovery	https://github.com/GoekeLab/bambu#De-novo-transcript-discovery
Storing and using preprocessed files (rcFiles)	https://github.com/GoekeLab/bambu#Storing-and-using-preprocessed-files-rcFiles
Tracking read-to-transcript assignment	https://github.com/GoekeLab/bambu#Tracking-read-to-transcript-assignment
Training a model on another species/dataset and applying it	https://github.com/GoekeLab/bambu#Training-a-model-on-another-speciesdataset-and-applying-it
Quantification of gene expression	https://github.com/GoekeLab/bambu#Quantification-of-gene-expression
Including single exons	https://github.com/GoekeLab/bambu#Including-single-exons
Fusion gene/isoform detection	https://github.com/GoekeLab/bambu#Fusion-geneisoform-detection
bambu Arguments	https://github.com/GoekeLab/bambu#Bambu-Arguments
Output Description	https://github.com/GoekeLab/bambu#Output-Description
Release History	https://github.com/GoekeLab/bambu#Release-History
Citation	https://github.com/GoekeLab/bambu#Citation
Contributors	https://github.com/GoekeLab/bambu#Contributors
	https://github.com/GoekeLab/bambu#installation
	https://github.com/GoekeLab/bambu#general-usage
here	https://github.com/GoekeLab/sg-nex-data/blob/master/docs/SG-NEx_Bambu_tutorial.md
Storing and using preprocessed files (rcFiles)	https://github.com/GoekeLab/bambu#Storing-and-using-preprocessed-files-rcFiles
Use precalculated annotation objects	https://github.com/GoekeLab/bambu#Use-precalculated-annotation-objects
De-novo transcript discovery	https://github.com/GoekeLab/bambu#De-novo-transcript-discovery
Modulating the sensitivity of discovery (pre and post analysis)	https://github.com/GoekeLab/bambu#Modulating-the-sensitivity-of-discovery-pre-and-post-analysis
Arguments	https://github.com/GoekeLab/bambu#Arguments
Output	https://github.com/GoekeLab/bambu#Output
	https://github.com/GoekeLab/bambu#transcript-discovery-only-no-quantification
Output	https://github.com/GoekeLab/bambu#Output
Modulating the sensitivity of discovery (pre and post analysis)	https://github.com/GoekeLab/bambu#Modulating-the-sensitivity-of-discovery-pre-and-post-analysis
	https://github.com/GoekeLab/bambu#using-precalculated-annotation-objects
	https://github.com/GoekeLab/bambu#running-multiple-samples
ncore	https://github.com/GoekeLab/bambu#bambu-arguments
Storing and using preprocessed files (rcFiles)	https://github.com/GoekeLab/bambu#Storing-and-using-preprocessed-files-rcFiles
	https://github.com/GoekeLab/bambu#modulating-the-sensitivity-of-discovery-pre-and-post-analysis
Training a model on another species/dataset and applying it	https://github.com/GoekeLab/bambu#Training-a-model-on-another-speciesdataset-and-applying-it
“Transcript discovery only”	https://github.com/GoekeLab/bambu#transcript-discovery-only-no-quantification
	https://github.com/GoekeLab/bambu#output
Output Description	https://github.com/GoekeLab/bambu#Output-Description
Storing and using preprocessed files (rcFiles)	https://github.com/GoekeLab/bambu#Storing-and-using-preprocessed-files-rcFiles
	https://github.com/GoekeLab/bambu#visualization
	https://github.com/GoekeLab/bambu/blob/devel/figures/plotTranscript.PNG
	https://github.com/GoekeLab/bambu/blob/devel/figures/plotGene.PNG
Running multiple samples	https://github.com/GoekeLab/bambu#Running-multiple-samples
	https://github.com/GoekeLab/bambu/blob/devel/figures/plotHeatMap.PNG
	https://github.com/GoekeLab/bambu/blob/devel/figures/plotPCA.PNG
	https://github.com/GoekeLab/bambu#bambu-advanced-options
paper	https://www.biorxiv.org/content/10.1101/2022.11.14.516358v1
	https://github.com/GoekeLab/bambu#using-a-pretrained-model
Training a model on another species/dataset and applying it	https://github.com/GoekeLab/bambu#Training-a-model-on-another-speciesdataset-and-applying-it
	https://github.com/GoekeLab/bambu#de-novo-transcript-discovery
Using a pretrained model	https://github.com/GoekeLab/bambu#Using-a-pretrained-model
Training a model on another species/dataset and applying it	https://github.com/GoekeLab/bambu#Training-a-model-on-another-speciesdataset-and-applying-it
Modulating the sensitivity of discovery (pre and post analysis)	https://github.com/GoekeLab/bambu#Modulating-the-sensitivity-of-discovery-pre-and-post-analysis
Modulating the sensitivity of discovery (pre and post analysis)	https://github.com/GoekeLab/bambu#Modulating-the-sensitivity-of-discovery-pre-and-post-analysis
	https://github.com/GoekeLab/bambu#storing-and-using-preprocessed-files-rcfiles
here	https://bioconductor.org/packages/release/bioc/html/BiocFileCache.html
	https://github.com/GoekeLab/bambu#tracking-read-to-transcript-assignment
	https://github.com/GoekeLab/bambu#training-a-model-on-another-speciesdataset-and-applying-it
Storing and using preprocessed files (rcFiles)	https://github.com/GoekeLab/bambu#Storing-and-using-preprocessed-files-rcFiles
	https://github.com/GoekeLab/bambu#quantification-of-gene-expression
	https://github.com/GoekeLab/bambu#including-single-exons
	https://github.com/GoekeLab/bambu#fusion-geneisoform-detection
JAFFAL	https://github.com/Oshlack/JAFFA
	https://github.com/GoekeLab/bambu#bambu-arguments
	https://github.com/GoekeLab/bambu#output-description
	https://github.com/GoekeLab/bambu#release-history
issue	https://github.com/GoekeLab/bambu/issues/447
issue	https://github.com/GoekeLab/bambu/issues/505
issue	https://github.com/GoekeLab/bambu/issues/380
issue	https://github.com/GoekeLab/bambu/issues/450
	https://github.com/GoekeLab/bambu#citation
https://doi.org/10.1038/s41592-023-01908-w	https://doi.org/10.1038/s41592-023-01908-w
	https://github.com/GoekeLab/bambu#contributors
Ying Chen	https://github.com/cying111
Andre Sim	https://github.com/andredsim
Yuk Kei Wan	https://github.com/yuukiiwa
Keith Yeo	https://github.com/keithyjy
Min Hao Ling	https://github.com/lingminhao
Jonathan Goeke	https://github.com/jonathangoeke
	https://github.com/GoekeLab/bambu/blob/devel/figures/bambu_design_highres.png
rna-seq	https://github.com/topics/rna-seq
r	https://github.com/topics/r
nanopore	https://github.com/topics/nanopore
bioconductor	https://github.com/topics/bioconductor
transcriptomics	https://github.com/topics/transcriptomics
rna-seq-analysis	https://github.com/topics/rna-seq-analysis
transcript-quantification	https://github.com/topics/transcript-quantification
bambu	https://github.com/topics/bambu
long-reads	https://github.com/topics/long-reads
nanopore-sequencing	https://github.com/topics/nanopore-sequencing
transcript-reconstruction	https://github.com/topics/transcript-reconstruction
Readme	https://github.com/GoekeLab/bambu#readme-ov-file
GPL-3.0 license	https://github.com/GoekeLab/bambu#GPL-3.0-1-ov-file
Please reload this page	https://github.com/GoekeLab/bambu
Activity	https://github.com/GoekeLab/bambu/activity
Custom properties	https://github.com/GoekeLab/bambu/custom-properties
27 forks	https://github.com/GoekeLab/bambu/forks
Report repository	https://github.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FGoekeLab%2Fbambu&report=GoekeLab+%28user%29
Releases 6	https://github.com/GoekeLab/bambu/releases
bambu v3.12.1-Bioconductor release Latest Jan 16, 2026	https://github.com/GoekeLab/bambu/releases/tag/v3.12.1
+ 5 releases	https://github.com/GoekeLab/bambu/releases
Packages 0	https://github.com/orgs/GoekeLab/packages?repo_name=bambu
Please reload this page	https://github.com/GoekeLab/bambu
Please reload this page	https://github.com/GoekeLab/bambu
Contributors	https://github.com/GoekeLab/bambu/graphs/contributors
Please reload this page	https://github.com/GoekeLab/bambu
R 98.1%	https://github.com/GoekeLab/bambu/search?l=r
C++ 1.9%	https://github.com/GoekeLab/bambu/search?l=c%2B%2B
	https://github.com
Terms	https://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacy	https://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Security	https://github.com/security
Status	https://www.githubstatus.com/
Community	https://github.community/
Docs	https://docs.github.com/
Contact	https://support.github.com?tags=dotcom-footer

Viewport: width=device-width

URLs of crawlers that visited me.