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Dear all,
I obtained CNV results using nanopore reads (cov : ~50x, N50 : ~40kb).
However, there was big difference between results of qdnaseq and spectre as shown below.
qdnaseq : 4 CNVs
spectre…
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Hello!
I am running numbat on 36 lung tumor cryo visium reactions. My normal reference is a at tumor-adjacent "normal" visium reaction that has been confirmed to be tumor-free by a pathologist. My…
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The canvas object canbe configured in its properties to be able to go as low as 1 pixel in height and/or width, but PlugData has this arbitrary higher minimum of '9'
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I created a MSet combining EPICv2 with EPICv1 and/or 450K.
I created different annotation using CNV.create_anno with different array types - "EPICv2"/"EPIC"/"450k"/"overlap"
The overlap options see…
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Hi,
I have an issue running the code below with the mouse dataset.
gsc
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Dear All,
I'm running the code for inferCNV and everything gets generated correctly but in all the heatmaps generated the reference cell heatmap is missing.
The code I'm using for the run i…
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### Is this the right place to submit this?
- [X] This is not a security vulnerability or a crashing bug
- [X] This is not a question about how to use Istio
### Bug Description
I installed istio ve…
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Af1.x CNV releases will be considered complete without DRCs, only including HMM data and coverage calls.
I think the meaning of the pre-release `pre` arg, e.g. `Af1(pre=True)` will correspond to a …
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Number of communities: 17
Elapsed time: 52 seconds
Adding the partition
Using eps = NA
Error in if (firstval == -1) { : missing value where TRUE/FALSE needed
In addition: Warning message:
In as…
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It seems that the bulk_clones plot is sometimes missing the CNV state colors legend. Is that expected or a bug?
For example, here is the plot from the [mouse tutorial](https://kharchenkolab.github.…