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Hi,
When I ran scAbsolute with the default ploidy window I noticed that a lot of cells (~50%) had copy number of 1 across the genome, which is not something we expect to see in the samples (blood c…
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I already use `--AA_runmode` to stop create the output for SV visualization. But still show process of SV View and stuck here for 5days. :
```
[MOSEK:INFO] Beginning MOSEK call
[root:INFO] …
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we need to
1) integrate the raw counts to
2) cluster the data and
3) use the existing annotation to label each cluster.
- I will provide you with this pipeline so you can try to execute it …
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Hi,
First of all, thanks for making STARSolo.
Is there any way to get HDF5 as output from STARSolo pipeline after mapping/counting 10x droplet data?
Or any other way to get each individual tran…
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Hi! Thanks for providing a python-based version of CARLIN pipeline. We want to modify the arguments to run on our own sequencing data and reference from a different experiment protocol. However, I can…
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Thanks you for developing snapATAC tools,
and i have a question:
I followed the "Integrative Analysis of PBMC scATAC-seq and scRNA-seq" pipeline.
1. drawing the prediction score in histogram…
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We will generate a new Cell Marker ODK repo to manage markers for CL & CL-KG : - cellmark
The first aim for this repo will be to generate NS-Forest markers following standard patterns developed for…
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Hello,
1) I'd like to have a little more clarity on the QCs and parameters used to generate the cellbin UMAP on the SAW report.
I know stereopy is used, but I would like to know the values of th…
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Probably a new pipeline entirely, and one that could follow directly after the current single_cell_RNAseq processing pipeline.
The primary goal will be separating outputs from the current pipeline pe…
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I'm working on this and would like to incorporate some feedback about decision-making from one of the end-of-course surveys. Here's what it said:
_I think it would be incredibly useful if you could…