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Hi,
It looks like export theta is no longer functional with pandas >= 1.0, as I get this error when trying to run cnvkit.py export theta:
`
KeyError: 'Passing list-likes to .loc or [] with any …
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Hello to all wwylab group
I am currently working on equine embryos. We collected embryos from mares of different conditions at the stage of the expanded blastocyst (D8). At this stage, the embryo i…
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This is kind of different from the previous discussions because it specifically mentions targeted panels. Lots of methods already present in bcbio require at least exome-level coverage (TitanCNA for s…
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Hello,
For many samples, PureCN worked well but for one of the samples, it's throwing error. I have attached log file here [Sample_1-DNA.PureCN2.log](https://github.com/lima1/PureCN/files/4815108/…
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Dear Simone,
Congratulations for the tool, it is great being able to call allele-specific copy number in single cells and get the most of the data. At our lab, we have generated standard single-cell…
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Hi Gavin,
Thanks for your previous suggestions and I can run TitanCNA using snakemake pipeline successfully now. I have some questions about the parameters in snakemake pipeline:
1. First is about…
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Hi,
I just had two questions about what the minimum region length that PureCN can use? I see in `filterIntervals` you set a default minimum of 5bp - does this imply any size region (as long as it i…
waemm updated
5 years ago
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GIven the interest in studies that involve tumor heterogeneity / subclonality, currently bcbio offers "out of the box" support for both somatic variants and CNVs. A useful metric that can be combined …
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**General information about Sequenza**
Sequenza is a software package that uses paired tumor-normal DNA-seq data (WXS/WGS) for estimation of tumor cellularity (purity) and ploidy. Furthermore, it i…
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Hi there,
I was thinking about the following approach and was wondering on your opinion:
To further refine the identification of cell fractions/ tissue fractions in my bulk RNAseq samples I thou…