[MIG2025] Introduction to imaging-based spatial transcriptomics analysis

[bioc-workshop-dev]

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General Notes

This repository serves as a mostly automated pipeline for deploying workshops
to the Bioconductor Workshop.

Bot Commands

Issues in this repository are monitored to by a bot. All commands need to be
written on the first line of the comment, in a single line.

Example Docker Request

/request
  id='tidybioc2023'
  title='Tidy Transcriptomics'
  description='For Single-Cell RNA Sequencing Analyses'
  section='Smorgasbord 2023'
  source='https://github.com/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics'
  docker='ghcr.io/tidytranscriptomics-workshops/bioc2023_tidytranscriptomics:latest'

Note. The example /request is on multiple lines for readability.

Additional Workshop Information

Expected Number of Participants: 30

Workshop Date(s): August 13, 2025 - August 14, 2025

Workshop Start Time (approx.): 09:00

[bioc-workshop-dev]

READ ONLY: DO NOT EDIT ## /request id="CosMxSpatialAnalysisWorkshop" title="Introduction to imaging-based spatial transcriptomics analysis" description="This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight." section="MIG2025" startfile="README.md" source="https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop" docker=":" pkglist="" vignettes=""

[almahmoud]

/test id="mig2025spatial" title="Introduction to imaging-based spatial transcriptomics analysis" description="This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight." section="MIG2025" startfile="vignettes/workflow_spatial_cosmx.Rmd" source="https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop" pkglist="bhuvad/CosMxSpatialAnalysisWorkshop"

[almahmoud]

AUTO-GENERATED RESPONSE
Your request has been received and has passed initial screening. ✨

Below are the detected values:

id='mig2025spatial'
title='Introduction to imaging-based spatial transcriptomics analysis'
description='This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight.'
section='MIG2025'
source='https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop'
docker=''
port='8787'
command='echo "setwd(\"/home/rstudio\"); setHook(\"rstudio.sessionInit\", function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = \"append\")" > /home/rstudio/.Rprofile; /init'
pkglist='bhuvad/CosMxSpatialAnalysisWorkshop'
vignettes=''

If these are as expected, no further action is needed at this time. Please wait for an admin's response.
If any changes are needed, please re-run the /request action with desired values.

[almahmoud]

AUTO-GENERATED RESPONSE
Action Log
Your request has passed initial checks and is being built and/or deployed to the test instance.
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[almahmoud]

AUTO-GENERATED RESPONSE
Action Log
Your workshop has been successfully deployed to the test instance. ✨
Please test your workshop on the development instance and notify us via comment when you deem it ready for public consumption on the production instance.

[almahmoud]

/test id="mig2025spatial" title="Introduction to imaging-based spatial transcriptomics analysis" description="This workflow package shows how a basic analysis of spatial transcriptomics datasets is performed to gain biological insight." section="MIG2025" startfile="vignettes/workflow_spatial_cosmx.Rmd" source="https://github.com/bhuvad/CosMxSpatialAnalysisWorkshop" pkglist="bhuvad/CosMxSpatialAnalysisWorkshop" vignettes="vignettes/workflow_spatial_cosmx.Rmd"

[almahmoud]

AUTO-GENERATED RESPONSE
Action Log
Your request has passed initial checks and is being built and/or deployed to the test instance.
Please wait further updates.

[almahmoud]

AUTO-GENERATED RESPONSE
Action Log
Your workshop has been successfully deployed to the test instance. ✨
Please test your workshop on the development instance and notify us via comment when you deem it ready for public consumption on the production instance.