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In D4.1, we identifies these clonal analyses:
- [x] #91
- [ ] Clone ranked abundance distribution
- [ ] Clone frequencies
- [ ] Clone size
- [ ] Clonal shift and clonal drift
- [ ] Public clon…
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## 🚀 Feature
Allow plotting of "clonal trees" for bcell data, rooted on the germline.
## Motivation
B-cell repertoires are interesting because of SHM - you can group together different clonot…
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For `pipelineCNA()` a synthetic baseline is calculated per-sample. This can be an issue when you have a large dataset and have to run single samples for computational reasons as the baseline is differ…
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Hi, I read the your three research papers, These works will surely promote our understanding of tumor evolution.
- The evolution of lung cancer and impact of subclonal selection in TRACERx
- Clonal…
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Dear developers,
I want to use CNV to build phylogenetic tree. In infercnv, they do HMM to predict copy state of region then do clonal evolution analysis. But in copykat it still is a cnv score. How …
hahia updated
2 years ago
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`chr11 42923973 Minda_16 N . PASS SVLEN=1307;SVTYPE=INS;SUPP_VEC=ONT_severus_INS11155,ONT_Sniffles2.INS.17CMA,PB_Sniffles2.INS.182MA,PB_severus_INS9704,ONT_i_49,ONT_ID_39275_1,PB_i_127,PB_ID_49300_1
…
jzook updated
1 month ago
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Hello
I am trying to figure out how I can get the `ntot` required for clonality analysis
I have `ploidy`, `purity`, `major` and `minor allele copy number`
I googled for `ntot` which googling …
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Hello,
First of all, thank you for the very nice tool you have created; it has been very useful in my research!
I would like to ask for your assistance with a couple of issues I've encountered:
…
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Hi, I'm new to pyclone and I would like to use it to inferring AML clonal architecture from tumor-only targeted DNA sequencing samples.
I'm not sure how to get information about major and minor c…
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Hello,
Thanks for developing the tool. I was able to run without problems the 'Cluster' module for 39 samples individually (each sample separately) using the code:
`./PhylogicNDT.py Cluster -i ${i…