Diana Lin

bmcite progenitor cell types

1

I am trying to sort bone marrow cells into these categories: ```r celltypes

Cannot use buildReferenceFromSeurat with RunHarmony v1.0.3

1

I am trying to build a symphony reference using an existing Seurat object that I've already run harmony on. However, `RunHarmony` no longer produces anything in the `misc` slot of...

Difference between bin/bs_call and gemBSbinaries/bs_call?

3

What is the difference between these two binaries? ``` /home/dlin/.conda/envs/gembs/bin/bs_call /home/dlin/.conda/envs/gembs/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call ``` I've noted that the first one does not have options such as `-O` and `--contig-sizes`. The .vcf generated...

System.Error::Signal raised (no=11) using bs_call

2

With this command, I'm encountering an error: ```shell /usr/local/anaconda/lib/python3.9/site-packages/gemBS/gemBSbinaries/bs_call -r /ref/hg38_no_alt.gemBS.ref \ -n TGACCA \ --contig-bed /out_dir///calls/TGACCA/contigs_TGACCA_chr4.bed \ --contig-sizes /ref/hg38_no_alt.contig.sizes \ --report-file /out_dir///calls/TGACCA/TGACCA_chr4.json \ --right-trim 0 \ --left-trim 0 \...

Add support for spoilers in text commands

3

I'd like support for spoilers when using text commands just as is available with slash commands. By updating the prefix to include the two pipes, the bot still recognizes the...

Errors when using EnhancedVolcano with plotly::ggplotly

1

I've verified that my plot is infact a ggplot object: ``` > class(p) [1] "gg" "ggplot" ``` Most ggplot objects can be made interactive by doing: ``` plotly::ggplotly(p) ``` However,...

RunAzimuth error: Error in idx[i, ] <- res[[i]][[1]]

7

When using `RunAzimuth`: ```r DefaultAssay(obj)