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Hi Remi,
I am having more trouble with gene name errors in v 1.4 than 1.2. Clearly. the gene COX2 is in the ref list. Any ideas? I could use --new genes or --ignore but wondering if I am missing so…
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Currently in the file structure for `scRNA-seq`, we have some reference files (eg mitochondrial genes) that hang out in `data/` directories, but these aren't exactly data! It would be a bit of a lift …
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This is a quick fix but users should know that when doing any kind of multiome analysis, `addGeneExpressionMatrix()` is not accurately calculating `Gex_MitoRatio`. There are two sources of error here …
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```python
mito_genes = adata.var_names.str.startswith('MT-')
adata.obs['percent_mito'] = np.sum(adata[:, mito_genes].X, axis=1).A1 / np.sum(adata.X, axis=1).A1
adata.obs['n_counts'] = adata.X.sum(a…
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#### Current behavior:
23 genes are discovered to be uncorrelated with their corresponding reactions in `Carnitine shuttle`.
| Gene | UniProtID | Reaction | GPR | Correlation| Manually che…
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Thank you for publishing codes of your paper. Could you provide the codes for pre-processing datasets?
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Here's what I get:
`
JK_lesion_raw and JK_lesion are matrix from Read10x
Soup_sample = SoupChannel(JK_lesion_raw, JK_lesion)
Soup_sample = setClusters(Soup_sample, setNames(meta$seurat_clusters,…
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I am trying to provide custom mitochondrial geneIDs for QCMetrics in runCellQC like so:
```
library(singleCellTK)
library(tidyverse)
sce
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At some point we may want to make a more comprehensive list of barcoding genes and their synonyms (also for use in the sequence ID tool, etc.)
Starting here (with a bit of help from AI):
[edited…
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currently there are 36 genes in human annotated to this which seems high
The definitions are inconsistent in how they are phrased, and whether they talk about starts or ends:
* [] GO:0140467 ! i…