Yiwei Niu

Suggestions: provide a detailed description about clonotype definition model

1

## 📚 Documentation Hi, I think it is necessary to have a doc for models of clonotype definitions, like the one in [scirpy](https://icbi-lab.github.io/scirpy/tcr-biology.html).

KeyError: 'MATEID'

4

Hi, I'm running svtyper on the output of Delly2. Then I got these error messages: ``` Traceback (most recent call last): File "/home/work01/tools/SVTyper/svtyper/svtyper", line 1808, in sys.exit(main()) File "/home/work01/tools/SVTyper/svtyper/svtyper", line...

How to put highlighted text just above the points?

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Hi Lilin, Thanks very much for developing this useful tool. I wonder if there is a way to add highlighed text labels right on top of the points, like [this...

Questions about the alignment of MashMap

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Hello, Following #6, I checked the outputs of MashMap using blastn and got some quesions with the alignment. I think I shoud open a new issue to understand the ouput...

Hi, Thank you for this cool resource! In your recent [gnomAD SV paper](https://www.nature.com/articles/s41586-020-2287-8), the Figure 3 contains a idiogram of "meta-chromosome". I wonder if you could share it in this...

Plot control group and treatment group in different tracks, with group auto scale for each type of data.

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Hi, Thanks very much for developing this useful tool! I am plotting four tracks for ATAC-seq and RNA-seq data with one control and one treatment each (as below).  I...

Questions about the input expression matrix and threshold used in plotChromosomeHeatmap

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Hi, Thank you for this cool tool! I have three questions in using `CONICSmat`. 1. Is the input matrix must be `log2(CPM/10+1) normalized expression counts`? I tried the normalized data...

Hi, Thanks for developing this useful tool. I have two questions about understanding the output of qcSTR. 1. In the doc of qcSTR (https://trtools.readthedocs.io/en/latest/source/qcSTR.html):  > Can be used to...

Hi, Sometimes, people choose to paste two covariates into one like this: [Seurat V5 FindVariableFeatures() and HarmonyIntegration() Question](https://github.com/satijalab/seurat/issues/8325#issuecomment-1901125724). Considering the theta value (maybe also lambda) difference for one covariate or...

Hi, I am testing numbat on one patient with 68941 cells, and it ended with the following error: ```r Numbat version: 1.3.2.1 Scistreer version: 1.2.0 Running under parameters: t =...