Leonardo Collado-Torres

Document the existence of rworkflows externally

9

Hi, You might want to consider getting in touch with Kevin @kevinrue who has been working on some documentation on how to make a Bioconductor package. See https://bioconductor.github.io/bioc_mentorship_docs/bioc-package.html for more...

Related to #21 where I mentioned https://github.com/LieberInstitute/spatialLIBD/blob/e2f179bb7a3bfef30b319e84dc7702e3ce99aa67/.github/workflows/check-bioc.yml#L265, you might want to check out `cmdfun` by @snystrom. See also https://github.com/lcolladotor/dots/issues/1. Could be useful for https://github.com/neurogenomics/rworkflows/blob/master/R/use_workflow.R

Code of conduct template package + tools/packages for promoting a diverse and welcoming environment

6

Hi, I have a simple idea (I think) that could maybe grow into one or more packages/tools. The initial idea is the following one. I've seen that my co-workers have...

emptyDrops BioC 3.11 vs 3.12: different results with the OSCA pbmc 4k dataset

16

Hi Aaron et al, We (@Yalbibalderas @AnaBVA) noticed that the following code from OSCA returns different t-SNE plots. Eventually we narrowed down the issue to BioC 3.11 vs 3.12 (3.13...

Checking for co-expression of 2 genes

4

**Is your feature request related to a problem? Please describe.** A question I got after https://youtu.be/i5I_mFOsGks from a LIBD colleague was: how can I check for co-expression of 2 genes?...

req_error error triggered by downloading the lun spikein 2017 data (R 4.4, curl 8.6.0, bioc 3.19)

7

Hi, During a course we ran into this issue in @xxchenm's computer: ```R > library("scRNAseq") > sce.416b traceback() 7: stop("failed to save '", path, "'; ", status) 6: save_file(path =...

Comments on PR #111 + sharing trick we used for overlapping spots from overlapping capture areas

1

Hi `BayesSpace` authors, I saw PR https://github.com/edward130603/BayesSpace/pull/111 which seems interesting. I saw that you are changing some names, like `row` to `array_row` and stuff like that. I think that will...

Hi, Just as an FYI, we noticed that your `inst/CITATION` data is outdated. It still points to the preprint https://github.com/edward130603/BayesSpace/blob/8e9af8f2fa8e93518cf9ecee1ded9ab93e88fffd/inst/CITATION#L13 Best, Leo and @nick-eagles