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thelovelab / fishpond

Differential expression and allelic analysis, nonparametric statistics
https://thelovelab.github.io/fishpond
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add loadFry related code and example #6

Closed DongzeHE closed 3 years ago

DongzeHE commented 3 years ago

Hi Mike,

I wrote a function to read in the quantification output of alevin-fry USA mode and return a SingleCellExperiment object.

I have tested the function using tests/testthat/test_loadFry.R on a dummy example I created under inst/extdata/alevin/test_loadFry folder. Note that as rjson::fromJSON always returns me an error when reading the meta_info.json JSON file, I added jsonlite package as a dependency. Hope this will not bother you too much.

Moreover, I found a little typo (an extra comma) in vignettes/swish.Rmd, and I have fixed that, hope it helps

mikelove commented 3 years ago

Great! I'll test this out today

mikelove commented 3 years ago

Thanks!

I just added the Rd file (devtools doesn't automatically add this to the git repo, this happens to me all the time).

Happy to have a new fishpond contributor :)