spatialLIBD

spatialLIBD copied to clipboard

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.

lcolladotor

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.

lcolladotor

Born from the NAc project, we want to add support for visualizing multiple capture areas that have been stitched together.

lcolladotor

Improve internal code coverage using `covr` from the current 6% to at least 75% or higher for non-interactive functions.

lcolladotor

[BUG] Fail to obtain the spe data of DLPFC

2

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

YikaiLou

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`....

lahuuki

[BUG] Reporting of Missing Genes in Spot Plots multi-gene functionality

1

## The multi-gene function fails if the genes requested report no expression variation in some slides (samples). I have encountered an exception when certain genes are not present in some...

cyntsc

## Describe the bug Thank you for your work! I wanted to report that no data object is returned with `fetch_data(type='spe'). ### Provide a minimally reproducible example (reprex) ``` if...

dimalvovs

Currently using a registration variable with two groups causes `registration_wrapper()` to error out, as `registration_stats_anova` fails with k=2. To solve this, when k=2 the function now throws a warning and...

lahuuki

I greatly appreciate the funciton, just quickly pointing an minor issue - a confusing warning message. `Gene list with n < 25 may have insufficent power for enrichment analysis` followed...

boyiguo1