René's URL Explorer Experiment


Title: GitHub - FowlerLab/starcall-workflow: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline

Open Graph Title: GitHub - FowlerLab/starcall-workflow: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline

X Title: GitHub - FowlerLab/starcall-workflow: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline

Description: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline - FowlerLab/starcall-workflow

Open Graph Description: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline - FowlerLab/starc...

X Description: A snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline - FowlerLab/starc...

Opengraph URL: https://github.com/FowlerLab/starcall-workflow

X: @github

direct link

Domain: patch-diff.githubusercontent.com

route-pattern/:user_id/:repository
route-controllerfiles
route-actiondisambiguate
fetch-noncev2:a1507cb1-9820-5864-e306-c3ff0af0684a
current-catalog-service-hashf3abb0cc802f3d7b95fc8762b94bdcb13bf39634c40c357301c4aa1d67a256fb
request-idA7FE:CCC2B:E68442:1278F69:6990C588
html-safe-noncedd0605e1f00480d63a3eb955b898797186caa55c76a7463cfa0b2e2d2e76883e
visitor-payloadeyJyZWZlcnJlciI6IiIsInJlcXVlc3RfaWQiOiJBN0ZFOkNDQzJCOkU2ODQ0MjoxMjc4RjY5OjY5OTBDNTg4IiwidmlzaXRvcl9pZCI6IjIwMzI2Mjc0NTgyNDc4MDQyOTYiLCJyZWdpb25fZWRnZSI6ImlhZCIsInJlZ2lvbl9yZW5kZXIiOiJpYWQifQ==
visitor-hmaceffccf7f4117d7bb2ca480400ec32b506607f2209deeca48b8a46ac560f47025
hovercard-subject-tagrepository:954950446
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/FowlerLab/starcall-workflow
twitter:imagehttps://opengraph.githubassets.com/3b4fd5562b4295f39a3204be1ce412f3f22ec3564963d5615e873d1dc37aeba8/FowlerLab/starcall-workflow
twitter:cardsummary_large_image
og:imagehttps://opengraph.githubassets.com/3b4fd5562b4295f39a3204be1ce412f3f22ec3564963d5615e873d1dc37aeba8/FowlerLab/starcall-workflow
og:image:altA snakemake pipeline for the processing of in situ sequencing data. Provides improvements to stitching, alignment, and read calling all in a scalable and memory efficient pipeline - FowlerLab/starc...
og:image:width1200
og:image:height600
og:site_nameGitHub
og:typeobject
hostnamegithub.com
expected-hostnamegithub.com
None42c603b9d642c4a9065a51770f75e5e27132fef0e858607f5c9cb7e422831a7b
turbo-cache-controlno-preview
go-importgithub.com/FowlerLab/starcall-workflow git https://github.com/FowlerLab/starcall-workflow.git
octolytics-dimension-user_id9955205
octolytics-dimension-user_loginFowlerLab
octolytics-dimension-repository_id954950446
octolytics-dimension-repository_nwoFowlerLab/starcall-workflow
octolytics-dimension-repository_publictrue
octolytics-dimension-repository_is_forkfalse
octolytics-dimension-repository_network_root_id954950446
octolytics-dimension-repository_network_root_nwoFowlerLab/starcall-workflow
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
release848bc6032dcc93a9a7301dcc3f379a72ba13b96e
ui-targetfull
theme-color#1e2327
color-schemelight dark

Links:

Skip to contenthttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#start-of-content
https://patch-diff.githubusercontent.com/
Sign in https://patch-diff.githubusercontent.com/login?return_to=https%3A%2F%2Fgithub.com%2FFowlerLab%2Fstarcall-workflow
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%2FFowlerLab%2Fstarcall-workflow
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=FowlerLab%2Fstarcall-workflow
Reloadhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Reloadhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Reloadhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
FowlerLab https://patch-diff.githubusercontent.com/FowlerLab
starcall-workflowhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FFowlerLab%2Fstarcall-workflow
Fork 0 https://patch-diff.githubusercontent.com/login?return_to=%2FFowlerLab%2Fstarcall-workflow
Star 1 https://patch-diff.githubusercontent.com/login?return_to=%2FFowlerLab%2Fstarcall-workflow
MIT license https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/LICENSE
1 star https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/stargazers
0 forks https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/forks
Branches https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/branches
Tags https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tags
Activity https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/activity
Star https://patch-diff.githubusercontent.com/login?return_to=%2FFowlerLab%2Fstarcall-workflow
Notifications https://patch-diff.githubusercontent.com/login?return_to=%2FFowlerLab%2Fstarcall-workflow
Code https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Issues 0 https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/issues
Pull requests 0 https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/pulls
Actions https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/actions
Projects 0 https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/projects
Security 0 https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/security
Insights https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/pulse
Code https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Issues https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/issues
Pull requests https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/pulls
Actions https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/actions
Projects https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/projects
Security https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/security
Insights https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/pulse
Brancheshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/branches
Tagshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tags
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/branches
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tags
133 Commitshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/commits/master/
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/commits/master/
packageshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tree/master/packages
packageshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tree/master/packages
workflowhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tree/master/workflow
workflowhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/tree/master/workflow
.gitignorehttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/.gitignore
.gitignorehttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/.gitignore
.gitmoduleshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/.gitmodules
.gitmoduleshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/.gitmodules
LICENSEhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/LICENSE
LICENSEhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/LICENSE
constitchhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/constitch
constitchhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/constitch
default-config.yamlhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/default-config.yaml
default-config.yamlhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/default-config.yaml
readme.mdhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/readme.md
readme.mdhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/readme.md
requirements.txthttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/requirements.txt
requirements.txthttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/requirements.txt
run.shhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/run.sh
run.shhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/run.sh
starcallhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/starcall
starcallhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/blob/master/starcall
READMEhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
MIT licensehttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#starcall-stitching-alignment-and-read-calling-for-in-situ-sequencing-experiments
https://fowlerlab.github.io/starcall-docs/starcall.htmlhttps://fowlerlab.github.io/starcall-docs/starcall.html
https://fowlerlab.github.io/starcall-docs/constitch.htmlhttps://fowlerlab.github.io/starcall-docs/constitch.html
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#quick-start
https://visseq.gs.washington.edu/data_download/https://visseq.gs.washington.edu/data_download/
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#installation
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#installing-cellprofiler
https://cellprofiler.orghttps://cellprofiler.org
https://github.com/CellProfiler/CellProfiler/wiki/Conda-Installationhttps://github.com/CellProfiler/CellProfiler/wiki/Conda-Installation
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#download-testing-dataset
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#run-pipeline
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#expected-output
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#structure
https://fowlerlab.github.io/starcall-docs/starcall.htmlhttps://fowlerlab.github.io/starcall-docs/starcall.html
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#general-file-structure
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#nikon-microscope-inputs
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#general-input
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#auxillary-barcode-input
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#outputs
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#log-files
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#config-files
https://github.com/marrlab/BaSiChttps://github.com/marrlab/BaSiC
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#running-the-pipeline
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#complete-options-for-output-files
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#subset
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#section
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#tile-grids
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#phenotyping-options
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#parameters
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#steps-of-the-pipeline
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#extraction-from-the-nd2-file
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#alignment
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#stitching-full-well
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#stitching-into-tiles
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#cell-segmentation
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#merging-the-segmentation-grid
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#splitting-the-segmentation-grid
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#calling-reads
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#combining-reads
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#matching-reads-to-barcodes
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#merging-phenotype-tables
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#calculating-simple-features
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#calculating-features-with-cellprofiler
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#merging-calculated-features
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#merging-phenotype-tables-1
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#merging-phenotype-and-genotype
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#quality-control-steps
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#stitching-plots
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#read-quality-plots
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#cell-segmentation-overlay
https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#highlight-detected-sequencing-colonies
Readme https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#readme-ov-file
MIT license https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow#MIT-1-ov-file
Please reload this pagehttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow
Activityhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/activity
Custom propertieshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/custom-properties
1 starhttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/stargazers
1 watchinghttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/watchers
0 forkshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/forks
Report repository https://patch-diff.githubusercontent.com/contact/report-content?content_url=https%3A%2F%2Fgithub.com%2FFowlerLab%2Fstarcall-workflow&report=FowlerLab+%28user%29
Releaseshttps://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/releases
Packages 0https://patch-diff.githubusercontent.com/orgs/FowlerLab/packages?repo_name=starcall-workflow
Python 99.1% https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/search?l=python
Shell 0.9% https://patch-diff.githubusercontent.com/FowlerLab/starcall-workflow/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.