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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 …
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## INSTALL
pangenie]$ cd build/
build]$ cmake ..
-- The C compiler identification is GNU 9.3.0
-- The CXX compiler identification is GNU 9.3.0
-- Detecting C compiler ABI info
-- Detecting C co…
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Hi,
Thanks for the great tool and way less intimidating to install than previous version. It works!
Do you have a verbose mode, where the exact molecule position (in 3D) at east time step are wri…
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Edit: despite the title this link list now contains all kinds of reference material for benchmarking/normal-filtering SV (including CNV) calls on a population level as well on single sample (mostly ce…
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When data one alteration type are missing from the TCGA, the package returns a generic message:
> "No alteration to display for the selected tumor types and alteration types"
It would be more us…
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I am trying to run the example data:
```R
data_dir
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Hello,
I'm having difficulty interpreting regions for which homozygous deletions are called.
For regions assigned a copy number of 0 in the tumor (below from the `ratio.txt` file), some have a BAF …
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This is my first analysis and I ran FACETS on CT26 mouse tumors and Normal tissues (taken from literature). I obtain strange results because all the segments seems to be with 1 copy number (i expect…
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The SEG files generated by CNVkit could be used with GISTIC to identify recurring regions of gains and/or losses. However, GISTIC has been built with array CGH in mind, and so requires a so called "ma…