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TRAJ35-TRAJ35,2,0.00124146492862
TRAJ48-TRAJ48,34,0.0211049037865
TRAV1-TRAJ35,75,0.0465549348231
TRAJ35 - should not be here
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Hi -
By using the testing example provided in the package, I was able to generate successfully the tree.zip file, as well as a file named 'clonalFrequencies'. I assume this is where you'd get outp…
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Hi, I'm trying to run the copycat.
Following the code in manual (https://github.com/chrisamiller/copycat/, Usage), I have some problems when I running it.
I got the error msg below:
[1] "inferr…
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If you want to make use of the functionality that I've written on getting expression-based subtypes for a specified cancer type - check the `getBroadSubtypes` function in here:
https://github.com/w…
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If you want to make use of the functionality that I've written on getting the original GISTIC2 calls (not the one already mapped to genes) of specified peak type for a specified cancer type - check th…
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As discussed on our call, please submit a proposal for how to represent clonality information as a pull request that includes a markdown file in the `specs` directory. We can centralize discussion in…
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Hi, I have seen you submitted the package to Bioconductor, thanks for doing so.
In the README and in the vignette there are several references to your paper. Could you provide a link or a referenc…
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Hello,
I have been playing with superFreq and have been running it with default parameters. For the initial testing I ran it on 2 cases (each with 3 samples : 2 tumours and a paired normal ) with 3 s…
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I have tried with no success to set up the local building test.
With circleci build, I do not seem to have gcc in the build environment. Here is an example with fastree recipe incremented by 1.
`…
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Hi all,
Now that most of the hg38 reference files are in place (thanks for adding them up), I wonder which is the minimum command-line to apply to a wig file created from an hg38 bam file without a…