Stefano Mangiola

The job submission of the workflow is very inefficient because we are asking for much more memory than needed. It would be nice to profile memory consumption of the jobs...

Get sample ID (not donor ID)

4

## Description I was wondering if there is information in the metadata or elsewhere about sample identifier. Donor identifier is good, but the same donor can have samples for multiple...

This is to take @mikelove commit https://github.com/stemangiola/tidySummarizedExperiment/pull/94/commits/faf5585d2acdb13cb22e5b17549eab7ed3a536df to the other tidy transcriptomic packages @william-hutchison for tidySPE

I think it would be a great addition to allow DelayedArray as input to `singscore`, for very large-scale analyses. Thanks!

pseuodbulk file not found in the cloud - 3fe53a40-38ff-4f25-b33b-e4d60f2289ef

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This file does not exist apparently https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/pseudobulk-0.1.0/original/3fe53a40-38ff-4f25-b33b-e4d60f2289ef/assays.h5

cache for pseudobulk same as for single cell?

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@myushen I noticed that if I query pseudobulk ```r my_metadata |> get_pseudobulk(assays = "counts") ``` the data is stored in the wrong cache? ```r Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/pseudobulk-0.1.0/original/GSE122960/se.rds to /Users/mangiola.s/Library/Caches/org.R-project.R/R/CuratedAtlasQueryR/0.2.1/original/GSE122960/se.rds ``` I...

Similar to @myushen https://github.com/DavisLaboratory/singscore/blob/903177c62e42fff001fe4fdf0b34fc5d3bf924a5/R/singscore.R#L76 the preprint https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3

@myushen would you mind adding the citation to the article https://joss.theoj.org/papers/10.21105/joss.02472 to all methods (https://github.com/stemangiola/tidyHeatmap/blob/master/R/methods.R) like you did for the other pakcage? Thanks!