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Hello,
Section 1.3 of the README reads:
> At this point, we get
> - a scRNA-seq count matrix from cellranger (1.1) with automated filtered cells based on cellranger cutoffs for detecting empty …
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The current scRNA-seq notebook 01 starts to get into pretty high memory usage of ~4Gb with multiple copies of the large count matrix under different filtering conditions, etc. It might be good to add …
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Hi,
I am just wondering if this work flow works with 10x data?
Wilson
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Hi, I now want to use spatialscope as baseline, but it hardly works on the new dataset.
On the one hand the new dataset doesn't have cell type, I tried to use the clustering results as category label…
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The current directory structure for the scRNA module set looks something like this:
```
training-modules/scRNA-seq$ tree
.
├── 00-scRNA-seq_introduction.md
├── 01-normalizing_scRNA-seq.Rmd
├── 0…
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When I did cNMF in spatial transcriptomics, in which the n_counts of one spot could be smaller than scRNA-seq cell. It usually encounter that I have to drop many spots, due to there is no highly varai…
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I frequently work with single-cell multi-omics data (mostly scRNA-seq + CITE-seq, but scATAC-seq is also expected), and it is known that different modalities for the same samples requires separate seq…
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Hi!
Really cool package that's easy to use. I've already compared it to some prior selections using geneBasis and think I'd like to switch over. One of the things I'm I'd like to make sure I unders…
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Hi, thanks for the great tool!
I ran Numbat (v1.2.1) on a 10x scRNA-seq dataset. The program outputs the CNV plots ("panel_2.png") without reporting any error. However, the probabilities of each CN…
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Hi,
Thank you for creating such a wonderful tool! I am currently working with scRNA-seq data consisting of 8 million cells and I am particularly interested in analyzing 100 specific genes. I would …