Skip to content
New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Clean up mtx conversion code #310

Open
grst opened this issue Mar 5, 2024 · 0 comments · May be fixed by #369
Open

Clean up mtx conversion code #310

grst opened this issue Mar 5, 2024 · 0 comments · May be fixed by #369
Labels
enhancement New feature or request quality & consistency improve quality and reduce maintenance burden

Comments

@grst
Copy link
Member

grst commented Mar 5, 2024

Description of feature

The mtx conversion has grown organically over time and seems error-prone and overly complex.

Also with the new emptydrops #301 cell calling, matrices need to be transposed and back which is very annoying.

I suggest to streamline this by creating one "standardized" single-sample output per aligner (either mtx or h5 format), that is then read in by the downstream processes, such as empty drops, and conversion processes. Since this pipeline is going multimodal, we'll also want to support MuData output in addition to AnnData.

We can also explore if it's easier to obtain Seurat and SingleCellExperiment objects by converting from AnnData using e.g. anndataR instead of building them from scratch in different languages.

Related issues:

@grst grst added enhancement New feature or request quality & consistency improve quality and reduce maintenance burden labels Mar 5, 2024
@fmalmeida fmalmeida linked a pull request Sep 16, 2024 that will close this issue
8 tasks
@fmalmeida fmalmeida linked a pull request Sep 16, 2024 that will close this issue
8 tasks
Sign up for free to join this conversation on GitHub. Already have an account? Sign in to comment
Labels
enhancement New feature or request quality & consistency improve quality and reduce maintenance burden
Projects
None yet
Development

Successfully merging a pull request may close this issue.

1 participant