-
Hi,
Thank you for developing this tool which is quite easy to use!
I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have paired tumor and normal WES or RNA…
-
Hi @tianshilu,
Thanks for the method! I want to know how to use 'SClineager' to construct a tree with somatic mutations. Can you give me some suggestions?
Thank you very much!
-
Issue by @MaxUlysse, moved from SciLifeLab#666
- [ ] [ExpansionHunter](https://github.com/Illumina/ExpansionHunter) for estimating repeat sizes
- [ ] [QDNAseq](https://github.com/ccagc/QDNAseq) CN…
-
Hey,
Thanks for developing the SCmut tool. I am trying to use it on my own data, but my tumor- and normal- bulk bam file are all generated based on hg38. I try to use `gatk mutect2` to call somati…
-
Creating one issue with all feedback as not sure what all we want to actually work on for next steps..
✅**1 As of now, the function will break if the user enters samples = 'a data frame' instead of…
-
I want to upload my own column to cbioportal docker image. So, referring to the link[https://docs.cbioportal.org/5.1-data-loading/data-loading/file-formats#mutation-data], I wrote the input files acco…
-
I am trying to use the chromoscope package in Jupyter Notebook to load my data and use the genome view. However the view is not loading and the genome is not displayed. Please see my notebook below: …
-
There'll be a new `SV_STATUS` field that'll indicate SOMATIC or GERMLINE, see [doc](https://docs.google.com/document/d/1kfih0P9gNrFoY_FfWl-x3cGOL98u7gh3T6I5ZU_6q14/edit). We should show this in the on…
inodb updated
7 months ago
-
Need a class that represents disease mutations (genetic variants, mendelian disease mutations, complex disease variants, cancer autosomal and somatic variants) that are mapped to `Position` and `Resid…
-
Hi,
I'm experimenting with running COMPASS (using CNVs) with multiple samples (3 samples), where the cells then come from different runs with MissionBio. A problem is that they got sequenced at dif…