Include datasets

[grst]

In GitLab by @grst on Mar 16, 2020, 15:08

Include demo datasets as part of the package (sctcrpy.datasets) similar to how it is done in scanpy.

Nice datasets to include:

10x

• [x] https://www.nature.com/articles/s41586-020-2056-8#data-availability
• [ ] 10x genomics demo datasets.

Smartseq2

• [ ] https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE75688 (500 cells of human breast cancer, FASTQ available)
• [ ] https://www.cell.com/immunity/pdf/S1074-7613(19)30001-9.pdf (mouse)

This is a prerequisite of making a nice tutorial.

[grst]

In GitLab by @grst on Mar 19, 2020, 09:24

changed the description

[grst]

In GitLab by @grst on Mar 20, 2020, 18:14

changed the description

[grst]

In GitLab by @szabogtamas on Mar 26, 2020, 10:36

If we want to make some of the datasets available online, https://cyverse.org/data-store might be an option. Especially, if the datasets are too big for GitHub.

[grst]

In GitLab by @grst on Mar 26, 2020, 10:40

That's interesting... who's financing that?

There's a hack to attach files up to 2GB to github-releases, which I would have gone for... But this might be a good alternative.

[grst]

In GitLab by @szabogtamas on Mar 26, 2020, 10:51

I don't know much about this background. The reason I have used it so far is that it can host data for custom tracks in UCSC genome browser

[grst]

In GitLab by @grst on Apr 6, 2020, 19:49

started downloading fastq files of the smartseq2 data... at some point we can run them though sandro's pipeline.

[grst]

In GitLab by @grst on Apr 8, 2020, 15:01

assigned to @grst

[grst]

Closed in favor of #198.

We will have a nice BCR Smart-seq2 dataset, I don't think there is an urgent reason to add more.