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theislab
Conversion between scRNA-seq objects
Hello, I ran into this weird behavior when running `readH5AD`. For some reason, every first invocation of `readH5AD` stalls up to the point of displaying the anndata version. However, if...
I'm trying to read a 600k cell h5ad file into a SingleCellExperiment object in R, but it's throwing a timeout error. Can I extend the timelimit? ``` Reading /.../.../.../.../.../.../.../PFC.h5ad [30.2s]...
Thanks for making it possible to read `h5ad` files into R. I had a few issues/questions after trying to get the raw count matrix from a public `h5ad` file. Some...
pinging interested parties @lmweber @drighelli @HelenaLC @ivirshup Nice to meet you all! I believe with some we crossed paths in some zoom dungeons or email thread. I'd like to use...
Picking up a point from a recent FOM meeting, is there any interest in performing more advanced IO based on semantic labelling? For a concrete example, I'm thinking of reading...
Not really sure what's going on here, but: ```r library(SingleCellExperiment) example(SingleCellExperiment) metadata(sce)$WHEE
Likely of interest to @rcannood. If R starts to get good support for zarr (https://github.com/zarr-developers/community/issues/18), would support for reading the AnnData's written to zarr be in scope here? Particularly for...
Reminder to do this now that https://github.com/grimbough/rhdf5/issues/79 has been fixed. To do: - Remove the `is_sparse()` check - Update tests - Remove code coverage guards
Pretty much as it says. Missing all the sparse bits and pieces for `obsp`, `varp` and the sparse layers; this is waiting on grimbough/rhdf5#80. Will need some testing, as usual;...
Hi Luke, I tried to load a single cell dataset from https://singlecell.broadinstitute.org/single_cell/study/SCP1052/covid-19-lung-autopsy-samples#study-summary, however I get the following error ``` > sce2 rhdf5::h5ls("lung.h5ad") group name otype dclass dim 0 / X...
