Rachel Ng

You can store different versions of coordinates in adata like so before you overwrite it ```python adata.obsm['X_umap_mod'] = adata.obsm['X_umap'].copy() ``` And then use `pl.embedding` to plot the embedding by specifying...

The `tl.rank_genes_groups` function already sorts genes by their statistic score from greatest to smallest. If you want to sort the genes by log fold change from greatest to smallest, you...

Looks like this has been fixed. There is an option now to compare absolute fold changes if you set `compare_abs=True`.

I have contacted Professor Kerby Shedden who had given GEE in Python workshops at UMich in the past. He has shared that UMich have migrated form box to dropbox so...

Thanks for the advice! The VCF file contained SNPs generated by joint calling on GVCFs. I used bcftols isec to get its intersection with cellSNP's list of common variants. This...

I have tried reducing the number of SNPs to ~300K but it still ran out of RAM. But then I wrote a python script to read vartrix outputs of ref...

Same issue as #60 @Trikzon suggested using dataview inline fields for adding metadata, but its not the same as using Obsidian's native support for aliases/tags. ``` {% persist "tags" %}...

Here is a proposed solution that I tested: ```python def get_uns_colors(data: Union[AnnData, MuData], key: str): uns_key = key + '_colors' if uns_key in data.uns: return data.uns[uns_key] def to_dtype_list(x, dtype, n,...

Looking at the publication for the dsb tool, Figure 4a shows some negative values for dsb normalized protein data. So it seems like we should expect some negative values. Link...

Thanks for your reply! Yes, we performed Nanopore sequencing on a library originally prepared for Illumina sequencing. After some thought I think it might be a good thing to specify...