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It appears that the cell line metadata for GDSC1000 (and likely other datasets, assuming they were processed in a similar manner) is corrupted some cell lines.
Specifically, cell lines which contai…
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Based on a survey of the variant types used in CIViC as a starting point:
- SNVs (single nucleotide variants). e.g. `R175H`
- MNVs (e.g. dinucleotide variants). e.g. `VHL c.364_365GC>AT`
- Insert…
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Hello,
I have an issue while running MANTIS on exome datasets.
I wrote the following code lines :
`python2.7 mantis.py -b ../../Test_MANTIS/genome_scan.bed --genome ../../Test_MSISensor/Indexe…
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Hello,
Thanks for this very helpful package. I have a question regarding accessing the subtype information associated with TCGA projects (in this example, specifically `COAD` but my question applie…
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Hi there,
since GDC release 23 there is a new readout for TCGA, 'Allele-specific Copy Number Segment'. It would be great if it were downloadable in TCGAbiolinks via:
```R
query.cnv = TCGAbiolin…
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Hi
I wonder if it is possible to include in balsamic pipeline the analysis of signatures and MSI
This is important for some pediatric cases
thanks
teresita
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Hi,
Thank you for your improvment for tumor-only analysis. Could you give us more informations about the method used please ?
Bests,
Elodie
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Repeat expansion variants were first introduced before v1.0, in #94. Back then they were using a separate ClinVar TSV dump. The next improvement will arrive in the upcoming v2.0 release and will use t…
tskir updated
2 years ago
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I think it's likely that there is a general expression pattern for how mutated a tumor is. For example, super mutated tumors may have wacky gene expression, solely because they're super mutated and no…
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A meningioma that is transmitted from the parents to an offspring. [ NCIT:P378 ]
This definition is not great because this is not a Mendelian disease and in real cases it is not possible to know wh…