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Hi all! I'm the author of the CRAN package [workflowr](https://github.com/jdblischak/workflowr). It combines literate programming (knitr and rmarkdown) and version control (Git, via git2r) to generate…
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Per discussion between @md and me and feedback from @cband:
Currently, the final somatic MAF contains 279 columns. These are not all necessary, and a few could be omitted or collapsed into single c…
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https://doi.org/10.1038/s41591-018-0177-5
> Visual inspection of histopathology slides is one of the main methods used by pathologists to assess the stage, type and subtype of lung tumors. Adenocar…
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Create a readme file in Patient Directory for users
Define what files can be found in box
Define what files can be found in the PSC
Perhaps a venn diagram illustrating file location
How Dups ar…
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Hi,
When calling NTCN on paired data, I am getting an error `"Less than two modes were found in the empirical density of C1 after removing %d modes that are too weak (density < %g): %d", nModes - n…
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`Purple` fails with the below error:
```
ERROR ~ Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:PURPLE_CALLING:PURPLE (220024755)'
Caused by:
Process `NFCORE_ONCOANALYSER:TARGETED:P…
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I used the facets and loved it a lot for speed and easy implementation. I am wondering is there a function to generate input files for pyclone (like the sequenza function sequenza2pyclone)? Thanks.
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Hi,
I would like to run inferCNV on my integrated Seurat object that has both my healthy liver sample and a cancerous liver sample. I am able to split the integrated Seurat object back into the in…
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Dear Christoffer and team,
Thank you for developing superfreq. It does pretty much everything we want from WES analysis. All those annotations are great :)
I have been looking at CNAsegments*.tsv. c…
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Starting to think about this in the context of generating a lot of 10x VDJ data... it seems we will want to (eventually) have a way for `Clone`s to contain `cell`s (see https://github.com/airr-communi…