19 Re-use of bulk RNA-seq methods for spatial data exercise

Instructor: Leo

Hot of the pre-print press! 🔥 Our latest work #spatialDLPFC pairs #snRNAseq and #Visium spatial transcriptomic data in the human #DLPFC building a neuroanatomical atlas of this critical brain region 🧠@LieberInstitute @10xGenomics #scitwitter
📰 https://t.co/NJWJ1mwB9J pic.twitter.com/l8W154XZ50
— Louise Huuki-Myers (@lahuuki) February 17, 2023

19.1 Spatial registration

Louise A. Huuki-Myers recently contributed a new vignette to spatialLIBD as noted on the package news / changelog: http://research.libd.org/spatialLIBD/news/index.html#spatiallibd-1132. To follow it, you might want to have the latest version of spatialLIBD installed. You can install it with this command:

BiocManager::install("LieberInstitute/spatialLIBD")

Alternatively, you could have a Bioconductor devel setup, but that’s beyond the scope of this course. Using the devel docker image at http://bioconductor.org/help/docker/ is probably the easiest option.

After installing this version of spatialLIBD, you should be able to run without any issues the code Louise explains at http://research.libd.org/spatialLIBD/articles/guide_to_spatial_registration.html. This same information is displayed at https://bioconductor.org/packages/devel/data/experiment/vignettes/spatialLIBD/inst/doc/guide_to_spatial_registration.html.

19.2 Exercise

Exercise: Follow the vignette on spatial registration. Do the results change when you use cutoff_merge_ratio = 0.1? What is this argument controlling?