[BioC2024] Spatial transcriptomic clustering with BANKSY

[bioc-workshop-dev]

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

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Additional Workshop Information

Expected Number of Participants: 30

Workshop Date(s): July 25, 2024 - July 25, 2024

Workshop Start Time (approx.): 14:45

[bioc-workshop-dev]

READ ONLY: DO NOT EDIT ## /request id="banksy07252024" title="Spatial transcriptomic clustering with BANKSY" description="Banksy is an R package that incorporates spatial information to cluster cells in a feature space" section="BioC2024" startfile="README.md" source="https://github.com/prabhakarlab/Banksy" docker=":" pkglist="aricode, data.table, dbscan, SpatialExperiment, SingleCellExperiment, SummarizedExperiment, S4Vectors, stats, matrixStats, mclust, igraph, irlba, leidenAlg (>= 1.1.0), utils, uwot, RcppHungarian" vignettes="https://prabhakarlab.github.io/Banksy/articles/parameter-selection.html, https://prabhakarlab.github.io/Banksy/articles/domain-segment.html, https://prabhakarlab.github.io/Banksy/articles/batch-correction.html, https://prabhakarlab.github.io/Banksy/articles/multi-sample.html"

[vipulsinghal02]

My apologies, in addition to the packages above, may we also include the following packages? Thanks!

Banksy
Seurat
scater
cowplot
ggplot2
scuttle
spatialLIBD
ExperimentHub
harmony,
knitr,
rmarkdown,
pals,
scran,
testthat (>= 3.0.0),
BiocStyle

[vipulsinghal02]

Hi! Just saw the discussion on slack. Guess we will just do the demo locally on our laptops, but will be using the vignettes from our public git repo. Is there a way to give conference attendees installation instructions for the package before the workshop?

[almahmoud]

@vipulsinghal02 what slack discussion are you referring to? Do you still want it added to the platform? Also, is this a package demo?

[vipulsinghal02]

Hi Alex,

My apologies for the lack of clarity. This is the discussion I was referring to.

Yes it is a package demo. I thought about it a bit more, and okay yes, lets add us to the platform. Using your cloud platform might be the easiest way after all.

Best,
Vipul

[almahmoud]

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy" vignettes="vignettes/*"

[almahmoud]

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[almahmoud]

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

[almahmoud]

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[almahmoud]

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

[almahmoud]

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[almahmoud]

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[almahmoud]

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[almahmoud]

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

[almahmoud]

P.S. This workshop is having its image build correctly but failing on push. Can build manually if needed, but trying to fix it to push to Dockerhub if fails to GHCR.io

[almahmoud]

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[almahmoud]

/test id="banksy07252024" title="Package Demo: Banksy" description="Spatial transcriptomic clustering with BANKSY" section="BioC2024" startfile="vignettes/parameter-selection.Rmd" source="https://github.com/prabhakarlab/Banksy" docker="ghcr.io/bioconductor/bioconductor:3.19" pkglist="prabhakarlab/Banksy"

[almahmoud]

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[almahmoud]

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[vipulsinghal02]

P.S. This workshop is having its image build correctly but failing on push. Can build manually if needed, but trying to fix it to push to Dockerhub if fails to GHCR.io

Hmm okay. Will keep an eye out for when it’s ready. We will have a local presentation ready to project from our laptop just in case.

Thanks a lot!!

[almahmoud]

I'm not entirely sure why this one gave so much trouble with the automatic tooling compared to others, but will dig into it later. I've added it manually, please test it up on the platform.

[vipulsinghal02]

Thanks a lot, Alex! Getting on the flight, so will have spotty internet for the next day or so, but will test it whenever I can.

Cheers,
Vipul