René's URL Explorer Experiment


Title: GitHub - Genentech/Islander: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings.

Open Graph Title: GitHub - Genentech/Islander: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings.

X Title: GitHub - Genentech/Islander: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings.

Description: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings. - Genentech/Islander

Open Graph Description: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings. - Genentech/Islander

X Description: [Nature Biotech '25] Disclose the evaluation limitations for cell embeddings. - Genentech/Islander

Mail addresses
wang.hanchen@gene.com

Opengraph URL: https://github.com/Genentech/Islander

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:774dfd24-a055-fbc5-17a5-a9dce9baeb49
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-id89C6:B54D0:93AB27:BE42C5:6990561F
html-safe-nonce0b41e81b67cb001a487bbc09b53dd4c1ab25419fd623a13361efafbdfe851caf
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiI4OUM2OkI1NEQwOjkzQUIyNzpCRTQyQzU6Njk5MDU2MUYiLCJ2aXNpdG9yX2lkIjoiNDg0NDk2NTYwNTUxMjU5OTA3MiIsInJlZ2lvbl9lZGdlIjoiaWFkIiwicmVnaW9uX3JlbmRlciI6ImlhZCJ9
visitor-hmac33df6dcff0d3e2163b3d0995080e4294a73e9010d8490d53451d7a05c472f8ea
hovercard-subject-tagrepository:727744084
github-keyboard-shortcutsrepository,copilot
google-site-verificationApib7-x98H0j5cPqHWwSMm6dNU4GmODRoqxLiDzdx9I
octolytics-urlhttps://collector.github.com/github/collect
analytics-location//
fb:app_id1401488693436528
apple-itunes-appapp-id=1477376905, app-argument=https://github.com/Genentech/Islander
twitter:imagehttps://opengraph.githubassets.com/625ed1684cb7556247f7a9444db34d410bf010799bfc53ce80783bb9cf521486/Genentech/Islander
twitter:cardsummary_large_image
og:imagehttps://opengraph.githubassets.com/625ed1684cb7556247f7a9444db34d410bf010799bfc53ce80783bb9cf521486/Genentech/Islander
og:image:alt[Nature Biotech '25] Disclose the evaluation limitations for cell embeddings. - Genentech/Islander
og:image:width1200
og:image:height600
og:site_nameGitHub
og:typeobject
hostnamegithub.com
expected-hostnamegithub.com
None42c603b9d642c4a9065a51770f75e5e27132fef0e858607f5c9cb7e422831a7b
turbo-cache-controlno-preview
go-importgithub.com/Genentech/Islander git https://github.com/Genentech/Islander.git
octolytics-dimension-user_id3913764
octolytics-dimension-user_loginGenentech
octolytics-dimension-repository_id727744084
octolytics-dimension-repository_nwoGenentech/Islander
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id727744084
octolytics-dimension-repository_network_root_nwoGenentech/Islander
turbo-body-classeslogged-out env-production page-responsive
disable-turbofalse
browser-stats-urlhttps://api.github.com/_private/browser/stats
browser-errors-urlhttps://api.github.com/_private/browser/errors
release3b33c5aedc9808f45bc5fcf0b1e4404cf749dac7
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/Genentech/Islander#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FGenentech%2FIslander
GitHub CopilotWrite better code with AIhttps://github.com/features/copilot
GitHub SparkBuild and deploy intelligent appshttps://github.com/features/spark
GitHub ModelsManage and compare promptshttps://github.com/features/models
MCP RegistryNewIntegrate external toolshttps://github.com/mcp
ActionsAutomate any workflowhttps://github.com/features/actions
CodespacesInstant dev environmentshttps://github.com/features/codespaces
IssuesPlan and track workhttps://github.com/features/issues
Code ReviewManage code changeshttps://github.com/features/code-review
GitHub Advanced SecurityFind and fix vulnerabilitieshttps://github.com/security/advanced-security
Code securitySecure your code as you buildhttps://github.com/security/advanced-security/code-security
Secret protectionStop leaks before they starthttps://github.com/security/advanced-security/secret-protection
Why GitHubhttps://github.com/why-github
Documentationhttps://docs.github.com
Bloghttps://github.blog
Changeloghttps://github.blog/changelog
Marketplacehttps://github.com/marketplace
View all featureshttps://github.com/features
Enterpriseshttps://github.com/enterprise
Small and medium teamshttps://github.com/team
Startupshttps://github.com/enterprise/startups
Nonprofitshttps://github.com/solutions/industry/nonprofits
App Modernizationhttps://github.com/solutions/use-case/app-modernization
DevSecOpshttps://github.com/solutions/use-case/devsecops
DevOpshttps://github.com/solutions/use-case/devops
CI/CDhttps://github.com/solutions/use-case/ci-cd
View all use caseshttps://github.com/solutions/use-case
Healthcarehttps://github.com/solutions/industry/healthcare
Financial serviceshttps://github.com/solutions/industry/financial-services
Manufacturinghttps://github.com/solutions/industry/manufacturing
Governmenthttps://github.com/solutions/industry/government
View all industrieshttps://github.com/solutions/industry
View all solutionshttps://github.com/solutions
AIhttps://github.com/resources/articles?topic=ai
Software Developmenthttps://github.com/resources/articles?topic=software-development
DevOpshttps://github.com/resources/articles?topic=devops
Securityhttps://github.com/resources/articles?topic=security
View all topicshttps://github.com/resources/articles
Customer storieshttps://github.com/customer-stories
Events & webinarshttps://github.com/resources/events
Ebooks & reportshttps://github.com/resources/whitepapers
Business insightshttps://github.com/solutions/executive-insights
GitHub Skillshttps://skills.github.com
Documentationhttps://docs.github.com
Customer supporthttps://support.github.com
Community forumhttps://github.com/orgs/community/discussions
Trust centerhttps://github.com/trust-center
Partnershttps://github.com/partners
GitHub SponsorsFund open source developershttps://github.com/sponsors
Security Labhttps://securitylab.github.com
Maintainer Communityhttps://maintainers.github.com
Acceleratorhttps://github.com/accelerator
Archive Programhttps://archiveprogram.github.com
Topicshttps://github.com/topics
Trendinghttps://github.com/trending
Collectionshttps://github.com/collections
Enterprise platformAI-powered developer platformhttps://github.com/enterprise
GitHub Advanced SecurityEnterprise-grade security featureshttps://github.com/security/advanced-security
Copilot for BusinessEnterprise-grade AI featureshttps://github.com/features/copilot/copilot-business
Premium SupportEnterprise-grade 24/7 supporthttps://github.com/premium-support
Pricinghttps://github.com/pricing
Search syntax tipshttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
documentationhttps://docs.github.com/search-github/github-code-search/understanding-github-code-search-syntax
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FGenentech%2FIslander
Sign up https://patch-diff.githubusercontent.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=Genentech%2FIslander
Reloadhttps://patch-diff.githubusercontent.com/Genentech/Islander
Reloadhttps://patch-diff.githubusercontent.com/Genentech/Islander
Reloadhttps://patch-diff.githubusercontent.com/Genentech/Islander
Genentech https://patch-diff.githubusercontent.com/Genentech
Islanderhttps://patch-diff.githubusercontent.com/Genentech/Islander
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FGenentech%2FIslander
Fork 25 https://patch-diff.githubusercontent.com/login?return_to=%2FGenentech%2FIslander
Star 122 https://patch-diff.githubusercontent.com/login?return_to=%2FGenentech%2FIslander
MIT license https://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/LICENSE.txt
122 stars https://patch-diff.githubusercontent.com/Genentech/Islander/stargazers
25 forks https://patch-diff.githubusercontent.com/Genentech/Islander/forks
Branches https://patch-diff.githubusercontent.com/Genentech/Islander/branches
Tags https://patch-diff.githubusercontent.com/Genentech/Islander/tags
Activity https://patch-diff.githubusercontent.com/Genentech/Islander/activity
Star https://patch-diff.githubusercontent.com/login?return_to=%2FGenentech%2FIslander
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FGenentech%2FIslander
Code https://patch-diff.githubusercontent.com/Genentech/Islander
Issues 0 https://patch-diff.githubusercontent.com/Genentech/Islander/issues
Pull requests 0 https://patch-diff.githubusercontent.com/Genentech/Islander/pulls
Actions https://patch-diff.githubusercontent.com/Genentech/Islander/actions
Projects 0 https://patch-diff.githubusercontent.com/Genentech/Islander/projects
Security 0 https://patch-diff.githubusercontent.com/Genentech/Islander/security
Insights https://patch-diff.githubusercontent.com/Genentech/Islander/pulse
Code https://patch-diff.githubusercontent.com/Genentech/Islander
Issues https://patch-diff.githubusercontent.com/Genentech/Islander/issues
Pull requests https://patch-diff.githubusercontent.com/Genentech/Islander/pulls
Actions https://patch-diff.githubusercontent.com/Genentech/Islander/actions
Projects https://patch-diff.githubusercontent.com/Genentech/Islander/projects
Security https://patch-diff.githubusercontent.com/Genentech/Islander/security
Insights https://patch-diff.githubusercontent.com/Genentech/Islander/pulse
Brancheshttps://patch-diff.githubusercontent.com/Genentech/Islander/branches
Tagshttps://patch-diff.githubusercontent.com/Genentech/Islander/tags
https://patch-diff.githubusercontent.com/Genentech/Islander/branches
https://patch-diff.githubusercontent.com/Genentech/Islander/tags
16 Commitshttps://patch-diff.githubusercontent.com/Genentech/Islander/commits/main/
https://patch-diff.githubusercontent.com/Genentech/Islander/commits/main/
datahttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/data
datahttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/data
jupyter_nbhttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/jupyter_nb
jupyter_nbhttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/jupyter_nb
metahttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/meta
metahttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/meta
res/scGraphhttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/res/scGraph
res/scGraphhttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/res/scGraph
scriptshttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/scripts
scriptshttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/scripts
srchttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/src
srchttps://patch-diff.githubusercontent.com/Genentech/Islander/tree/main/src
.gitignorehttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/.gitignore
.gitignorehttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/.gitignore
LICENSE.txthttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/LICENSE.txt
LICENSE.txthttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/LICENSE.txt
README.mdhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/README.md
README.mdhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/README.md
env.ymlhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/env.yml
env.ymlhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/env.yml
teaser.pnghttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/teaser.png
teaser.pnghttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/teaser.png
READMEhttps://patch-diff.githubusercontent.com/Genentech/Islander
MIT licensehttps://patch-diff.githubusercontent.com/Genentech/Islander
https://patch-diff.githubusercontent.com/Genentech/Islander#islander
https://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/teaser.png
https://patch-diff.githubusercontent.com/Genentech/Islander#citation
https://patch-diff.githubusercontent.com/Genentech/Islander#usage
scriptshttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/scripts
Paperhttps://www.science.org/doi/10.1126/science.add7046
Paperhttps://www.nature.com/articles/s41586-023-06252-9
Paperhttps://www.ncbi.nlm.nih.gov/pmc/articles/PMC7402042/
Paperhttps://www.sciencedirect.com/science/article/pii/S2666979X22001069?via%3Dihub
Paperhttps://www.sciencedirect.com/science/article/pii/S1534580720308868?via%3Dihub
Paperhttps://linkinghub.elsevier.com/retrieve/pii/S0092867422014155
Paperhttps://www.nature.com/articles/s44161-022-00183-w
Paperhttps://www.nature.com/articles/s41591-023-02327-2
Paperhttps://www.nature.com/articles/s41592-021-01336-8
Paperhttps://www.nature.com/articles/s42003-020-0922-4
Datahttps://cellxgene.cziscience.com/collections/283d65eb-dd53-496d-adb7-7570c7caa443
Datahttps://cellxgene.cziscience.com/collections/4195ab4c-20bd-4cd3-8b3d-65601277e731
Datahttps://atlas.fredhutch.org/fredhutch/covid/
Datahttps://cellxgene.cziscience.com/collections/348da6dc-5bf6-435d-adc5-37747b9ae38a
Datahttps://cellxgene.cziscience.com/collections/17481d16-ee44-49e5-bcf0-28c0780d8c4a
Datahttps://cellxgene.cziscience.com/collections/2d2e2acd-dade-489f-a2da-6c11aa654028
Datahttps://cellxgene.cziscience.com/collections/43b45a20-a969-49ac-a8e8-8c84b211bd01
Datahttps://cellxgene.cziscience.com/collections/6f6d381a-7701-4781-935c-db10d30de293
Datahttps://figshare.com/articles/dataset/Benchmarking_atlas-level_data_integration_in_single-cell_genomics_-_integration_task_datasets_Immune_and_pancreas_/12420968?file=24539828
Datahttps://cellxgene.cziscience.com/collections/c353707f-09a4-4f12-92a0-cb741e57e5f0
Process_Breast.ipynbhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/jupyter_nb/Process_Breast.ipynb
scripts/_Islander_SCL.shhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/scripts/_Islander_SCL.sh
scripts/_Islander_Triplet.shhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/scripts/_Islander_Triplet.sh
scGPThttps://github.com/bowang-lab/scGPT/tree/main/tutorials/zero-shot
Geneformerhttps://huggingface.co/ctheodoris/Geneformer/tree/main/examples
scFoundationhttps://github.com/biomap-research/scFoundation/tree/main/model
UCEhttps://github.com/snap-stanford/UCE
_nb/Geneformer_Skin.ipynbhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/jupyter_nb/Geneformer_Skin.ipynb
Fibroblast_Case.ipynbhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/jupyter_nb/Fibroblast_Case.ipynb
https://patch-diff.githubusercontent.com/Genentech/Islander#file-organization
https://patch-diff.githubusercontent.com/Genentech/Islander#stand-alone-scgraph-package-for-evaluations
scgraphhttps://pypi.org/project/scgraph-eval/
https://patch-diff.githubusercontent.com/Genentech/Islander#python
https://patch-diff.githubusercontent.com/Genentech/Islander#command-line
https://patch-diff.githubusercontent.com/Genentech/Islander#notebook
Datahttps://drive.google.com/file/d/1a2UF4V_INGMKayCoMErZG-_kq_KuZmjA/view?usp=drive_link
Notebookhttps://patch-diff.githubusercontent.com/Genentech/Islander/blob/main/jupyter_nb/scGraph-minimal.ipynb
https://patch-diff.githubusercontent.com/Genentech/Islander#contributing
Readme https://patch-diff.githubusercontent.com/Genentech/Islander#readme-ov-file
MIT license https://patch-diff.githubusercontent.com/Genentech/Islander#MIT-1-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/Genentech/Islander
Activityhttps://patch-diff.githubusercontent.com/Genentech/Islander/activity
Custom propertieshttps://patch-diff.githubusercontent.com/Genentech/Islander/custom-properties
122 starshttps://patch-diff.githubusercontent.com/Genentech/Islander/stargazers
4 watchinghttps://patch-diff.githubusercontent.com/Genentech/Islander/watchers
25 forkshttps://patch-diff.githubusercontent.com/Genentech/Islander/forks
Report repository https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FGenentech%2FIslander&report=Genentech+%28user%29
Releaseshttps://patch-diff.githubusercontent.com/Genentech/Islander/releases
Packages 0https://patch-diff.githubusercontent.com/orgs/Genentech/packages?repo_name=Islander
Jupyter Notebook 91.5% https://patch-diff.githubusercontent.com/Genentech/Islander/search?l=jupyter-notebook
Python 8.1% https://patch-diff.githubusercontent.com/Genentech/Islander/search?l=python
Shell 0.4% https://patch-diff.githubusercontent.com/Genentech/Islander/search?l=shell
https://github.com
Termshttps://docs.github.com/site-policy/github-terms/github-terms-of-service
Privacyhttps://docs.github.com/site-policy/privacy-policies/github-privacy-statement
Securityhttps://github.com/security
Statushttps://www.githubstatus.com/
Communityhttps://github.community/
Docshttps://docs.github.com/
Contacthttps://support.github.com?tags=dotcom-footer

Viewport: width=device-width


URLs of crawlers that visited me.