Stefano Mangiola

I get Package suggested but not available: 'EGSEA'

3

In `tidybulk` actions using rworkflows https://github.com/stemangiola/tidybulk/actions/runs/6900279764/job/18773171864?pr=302 I get ```r ❯ checking package dependencies ... ERROR Package suggested but not available: 'EGSEA' ```

geometric gating

2

@qclayssen would you like to bring your request to completion? These would be a great addition. Please let me know.

Improve performances and interface of `tidygate` for large single-cell objects

4

tidygate allows gating points from a tibble, visually procedurally and in a replicable way, compatibly with a pipe-oriented programming style https://github.com/stemangiola/tidygate With an arbitrarily large amount of points (1M cells),...

@myushen, please have a look at to sccomp package github page and similarly add this article in the CITATION file. https://www.biorxiv.org/content/10.1101/2023.06.08.542671v3

add get_pseudobulk API

4

We have suitable available for the whole atlas, we should built a function that delivers those to the user The interface would look like ```r metadata |> filter(...) |> get_pseudobulk()...

@myushen This is in reference to https://teams.microsoft.com/l/message/19:130d71a5-dc95-495c-b678-77fe3c8131c5_2c56e6fb-516c-470d-8000-2e655cd72bbc@unq.gbl.spaces/1710302042265?context=%7B%22contextType%22%3A%22chat%22%7D The solution is to Change the `get_SCE` function, but NOT the `import` function. Commit 1: - Create a function that takes a list...

file_id_db=="e427efe71e8e94de5b3e48eb98236323" fails

2

@multimeric This query fails ```r get_metadata() |> + filter(file_id_db=="e427efe71e8e94de5b3e48eb98236323") |> get_single_cell_experiment() ℹ Realising metadata. ℹ Synchronising files ℹ Downloading 2 files, totalling 0.06 GB ℹ Downloading https://object-store.rc.nectar.org.au/v1/AUTH_06d6e008e3e642da99d806ba3ea629c5/cellxgene-0.2.1-hdf5/original/e427efe71e8e94de5b3e48eb98236323/assays.h5 to /home/users/allstaff/mangiola.s/.cache/R/CuratedAtlasQueryR/0.2.1/original/e427efe71e8e94de5b3e48eb98236323/assays.h5 Error...

duplicate 'row.names' are not allowed

6

Hi @multimeric , I get this error for this query ```r library(CuratedAtlasQueryR) # For accessing curated atlas data library(tidyverse) # For data manipulation and visualization # Retrieve and process the...