16_spatialLIBD_lecture.Rmd

# Introduction to the world of spatially-resolved transcriptomics with Visium data

Instructor: Leo

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Thank you <a href="https://twitter.com/hashtag/GBD23?src=hash&amp;ref_src=twsrc%5Etfw">#GBD23</a> <a href="https://twitter.com/MinaRyten?ref_src=twsrc%5Etfw">@MinaRyten</a> <a href="https://twitter.com/LabGandhi?ref_src=twsrc%5Etfw">@LabGandhi</a> John Hardy 🇬🇧 for hosting us!🙌🏽<br><br>Hopefully our <a href="https://twitter.com/hashtag/deconvochallenge?src=hash&amp;ref_src=twsrc%5Etfw">#deconvochallenge</a> <a href="https://twitter.com/hashtag/spatialLIBD?src=hash&amp;ref_src=twsrc%5Etfw">#spatialLIBD</a> <a href="https://twitter.com/hashtag/spatialDLPFC?src=hash&amp;ref_src=twsrc%5Etfw">#spatialDLPFC</a> <a href="https://twitter.com/hashtag/Visium_SPG_AD?src=hash&amp;ref_src=twsrc%5Etfw">#Visium_SPG_AD</a> work + <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> 📦s + <a href="https://twitter.com/10xGenomics?ref_src=twsrc%5Etfw">@10xGenomics</a> <a href="https://twitter.com/LieberInstitute?ref_src=twsrc%5Etfw">@LieberInstitute</a> data will be useful to you<a href="https://twitter.com/eventsWCS?ref_src=twsrc%5Etfw">@eventsWCS</a> <a href="https://twitter.com/UCLchildhealth?ref_src=twsrc%5Etfw">@UCLchildhealth</a> <a href="https://twitter.com/TheCrick?ref_src=twsrc%5Etfw">@TheCrick</a> <a href="https://twitter.com/UCLIoN?ref_src=twsrc%5Etfw">@UCLIoN</a> <a href="https://twitter.com/ucl?ref_src=twsrc%5Etfw">@ucl</a> <a href="https://t.co/vJcpL4tcQK">pic.twitter.com/vJcpL4tcQK</a></p>&mdash; 🇲🇽 Leonardo Collado-Torres (@lcolladotor) <a href="https://twitter.com/lcolladotor/status/1661837334084460552?ref_src=twsrc%5Etfw">May 25, 2023</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

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`r BiocStyle::Biocpkg("SummarizedExperiment")` --> `r BiocStyle::Biocpkg("SingleCellExperiment")` --> `r BiocStyle::Biocpkg("SpatialExperiment")` --> `r BiocStyle::Biocpkg("spatialLIBD")`

## Community

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Are you analyzing spatially-resolved transcriptomics data? Visium from <a href="https://twitter.com/10xGenomics?ref_src=twsrc%5Etfw">@10xGenomics</a>? You might want to use <a href="https://twitter.com/hashtag/SpatialExperiment?src=hash&amp;ref_src=twsrc%5Etfw">#SpatialExperiment</a> which provides a common infrastructure fully compatible with <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a>&#39;s ecosystem <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a><br><br>More details? Open access paper 📜<a href="https://t.co/4Y2RN4Wz2z">https://t.co/4Y2RN4Wz2z</a> <a href="https://t.co/49wE5Dv5HF">https://t.co/49wE5Dv5HF</a> <a href="https://t.co/QpI4lvCF2r">pic.twitter.com/QpI4lvCF2r</a></p>&mdash; 🇲🇽 Leonardo Collado-Torres (@lcolladotor) <a href="https://twitter.com/lcolladotor/status/1520066354241449988?ref_src=twsrc%5Etfw">April 29, 2022</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>

<blockquote class="twitter-tweet"><p lang="en" dir="ltr">Our paper describing our package <a href="https://twitter.com/hashtag/spatialLIBD?src=hash&amp;ref_src=twsrc%5Etfw">#spatialLIBD</a> is finally out! 🎉🎉🎉<br><br>spatialLIBD is an <a href="https://twitter.com/hashtag/rstats?src=hash&amp;ref_src=twsrc%5Etfw">#rstats</a> / <a href="https://twitter.com/Bioconductor?ref_src=twsrc%5Etfw">@Bioconductor</a> package to visualize spatial transcriptomics data.<br>⁰<br>This is especially exciting for me as it is my first paper as a first author 🦑.<a href="https://t.co/COW013x4GA">https://t.co/COW013x4GA</a><br><br>1/9 <a href="https://t.co/xevIUg3IsA">pic.twitter.com/xevIUg3IsA</a></p>&mdash; Brenda Pardo (@PardoBree) <a href="https://twitter.com/PardoBree/status/1388253938391175173?ref_src=twsrc%5Etfw">April 30, 2021</a></blockquote> <script async src="https://platform.twitter.com/widgets.js" charset="utf-8"></script>