[BIOC2024] Multiscale ESDA with SpatialFeatureExperiment and Voyager

[bioc-workshop-dev]

DO NOT INCLUDE REQUESTS IN THE FIRST COMMENT. PLEASE POST THIS TEMPLATE UNCHANGED THEN FOLLOW ITS INSTRUCTIONS IN A NEW COMMENT

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: 0

Workshop Date(s): July 24, 2024 - July 22, 2024

Workshop Start Time (approx.): 11:00

[bioc-workshop-dev]

READ ONLY: DO NOT EDIT ## /request id="sfe2024" title="Multiscale ESDA with SpatialFeatureExperiment and Voyager" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="BIOC2024" startfile="README.md" source="https://github.com/lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:devel" pkglist="" vignettes=""

[lambdamoses]

/request id="sfe2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="BIOC2024" startfile="vignettes/workshop.Rmd" source="https://github.com/lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:devel" pkglist="" vignettes=""

[almahmoud]

AUTO-GENERATED RESPONSE Your request has been received but is currently failing initial screening. Please retry your request ensuring all parameters are passed in correctly.

[lambdamoses]

/request id="sfe2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="Bioc2024" startfile="vignettes/workshop.Rmd" source="https://github.com/lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:devel" pkglist="" vignettes=""

[almahmoud]

AUTO-GENERATED RESPONSE Your request has been received but is currently failing initial screening. Please retry your request ensuring all parameters are passed in correctly.

[lambdamoses]

/request id="sfe2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="Bioc2024" startfile="vignettes/workshop.Rmd" source="https://github.com/lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:devel"

[almahmoud]

AUTO-GENERATED RESPONSE Your request has been received but is currently failing initial screening. Please retry your request ensuring all parameters are passed in correctly.

[lambdamoses]

/request id="sfe2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="Bioc2024" startfile="vignettes/workshop.Rmd" source="lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:devel"

[almahmoud]

AUTO-GENERATED RESPONSE Your request has been received but is currently failing initial screening. Please retry your request ensuring all parameters are passed in correctly.

[lambdamoses]

/request id="sfe2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="Bioc2024" startfile="vignettes/workshop.Rmd" source="lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:latest"

[almahmoud]

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

Below are the detected values:

id='sfe2024'
title='Exploratory spatial data analysis from single molecules to multiple samples'
description='This workshop showcases new features in SpatialFeatureExperiment and Voyager, including support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations'
section='Bioc2024'
source='lambdamoses/SFEWorkshop2024'
docker='ghcr.io/lambdamoses/sfeworkshop2024:latest'
port='8787'
command='echo "setwd(\"/home/rstudio\"); setHook(\"rstudio.sessionInit\", function(newSession) { if (newSession) rstudioapi::filesPaneNavigate(getwd()) }, action = \"append\")" > /home/rstudio/.Rprofile; /init'
pkglist=''
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]

/test id="sfebioc2024" title="Exploratory spatial data analysis from single molecules to multiple samples" description="Using SpatialFeatureExperiment and Voyager with support for transcript spot geometries in rowGeometries, plotting transcript spots, aggregating transcript spots with a spatial grid or any geometry, aggregating cell level data with a spatial grid or any geometry, splitting SFE objects with geometries, and improved support for images and affine transformations" section="BioC2024" startfile="vignettes/workshop.Rmd" source="https://github.com/lambdamoses/SFEWorkshop2024" docker="ghcr.io/lambdamoses/sfeworkshop2024:latest"

[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. :sparkles: 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.

[lambdamoses]

The code works on the test instance and is ready for production, though I will continue to edit the text. What's the deadline to finalize everything?

[almahmoud]

You can make changes up until tomorrow afternoon ET time. Tomorrow when I land in Michigan, around 2 PM local time, I will freeze everything as I will be scaling up all the extra nodes, and caching all the containers on all the nodes