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Hi,
I'm trying to install scarHRD but since there is not sequenza package available nowadays, I got installing scarHRD the error:
ERROR: dependency ‘sequenza’ is not available for package ‘scarHRD’…
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When running reverse package depdencies checks, **QDNAseq** sometimes gives the following error:
```sh
* using R version 4.3.2 (2023-10-31)
* using platform: x86_64-pc-linux-gnu (64-bit)
* R was…
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Hi Dave,
I'm running SVTyper on output from Lumpy for hg38 whole genome samples with 50x depth, interested in finding Deletions and other SVs with a low false-positive rate. The purpose is for person…
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Ratio is the log-ratio of the likelihood between the most likely copy number and the second likely copy number. I'm still trying to optimize t1k-copynumber.py, so please interpret its re…
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Hi
I have a problem making plots.
I change my chromosomes names as chr001..2..3...
I change the script to include my numbers but the plot only show the last chromosome.
This the change a made in…
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Hi,
Thank you for this very useful package. As many of the CCLE lines have now been screened in Achilles experiments, I'm wondering whether any thought has been given to harmonizing and serving th…
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This goes later for sure, as it gets complicated/messy
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Hi,
I have generated a allele-specific segmentation file with CNVkit. I adapted the format to fit your input
"... allele-specific segmentation file with the following columns: 1st column: sample n…
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```
$ build-esi-g4ox/src/consgeo -g esi-g4ox/geom/issue_unique_bordersurface.gdml
gdml_file: esi-g4ox/geom/issue_unique_bordersurface.gdml
G4GDML: Reading 'esi-g4ox/geom/issue_unique_bordersurface.…
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Hi there,
I'm having some issues running amber and cobalt.
This is an issue with my java installation. Although I have a copynumber available in my version of R, java is not using this version of …