spatialLIBD
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LieberInstitute
Code for the spatialLIBD R/Bioconductor package and shiny app
As `spatialLIBD` lists provides access to several datasets through Dropbox, we want to upgrade this and provide access to the datasets through ExperimentHub by Bioconductor.
Based on the spatialDLPFC project, we decided that the heatmaps look better when made with `ComplexHeatmap`. We need to change all internal heatmaps to use this package.
Born from the NAc project, we want to add support for visualizing multiple capture areas that have been stitched together.
Improve internal code coverage using `covr` from the current 6% to at least 75% or higher for non-interactive functions.
hello, thank you for creating such an outstanding work.Recently, I wanted to input the datasets, but it shows an error: library(spatialLIBD) library(ExperimentHub) packageVersion("spatialLIBD") ehub ehub spe
Adding a function to aid/standardize the QC process of new `spe` objects based off of work in [Habenula_Visium](https://github.com/LieberInstitute/Habenula_Visium/blob/7fc73e8cb403bcaa035f2451602db3fc0f38b103/code/02_build_spe/02_exploratory_QCs.R#L188-L295), [spatial_NAc](https://github.com/LieberInstitute/spatial_NAc/blob/56c67e7c0421e6dcf71fe2db6ef2c7b62ed15e58/code/05_harmony_BayesSpace/02-compute_QC_metrics.R#L69-L128), and [Visium_SPG_AD](https://github.com/LieberInstitute/Visium_SPG_AD/blob/e13e1a3604aa2dc43d76fa6923541ef403b0b13d/code/07_spot_qc/05_qc_plots_revision.R#L89-L152). Utilizes `scater::isOutlier` on three metrics `log2(sum_umi)`, `log2(sum_gene)`, and `expr_chrM_ratio*100`....
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Code for the spatialLIBD R/Bioconductor package and shiny app