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From #7 we see that ZBTB16 & SLC39A1 are strongly anti-correlated in ORF data and CRISPR data, and it's novel (not seen in Evotec KG).
Zinc finger and BTB domain-containing protein 16
SLC: Zinc t…
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Im running the analysis on 14 BAM files 7 from tumor and 7 from its germline. which is in a
/mnt/d/AKU/FTP/BAM/.
I rand the following command to test the tool:
`./ximmer -v -nosim -c /mnt/d/AKU/…
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Hi, thanks for this great tool!
I am not able to run the somatic mutation calls for multiple libraries. I have two runs for the normal and two runs for the tumor. The seqmule pipeline generates the f…
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From the file in issue #7 [MorphMap_gene_gene_scoring_data_with_CRISPR.xlsx](https://github.com/broadinstitute/2023_12_JUMP_data_only_vignettes/files/13844874/MorphMap_gene_gene_scoring_data_with_CRI…
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Dear Philip / noise-free-cnv team,
I'm working with about 1000 SNP6.0-assayed tumor (cell line) samples that are presumptively quite noisy, mainly because there are no normal samples for reference.…
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Hi,
I am trying to use infercnvpy on my single-cell dataset, but when I run:
cnv.tl.infercnv(
adata,
reference_key="leiden_1.0",
reference_cat='12',
)
I get the error message: …
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Long TODO lists don't get done.
We are trying to keep an issue open if a real effort is happening to resolve it.
The below priority list gives a sense of where bcbio is heading in the next two rele…
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I've been looking through the source of tag from file, and based on the test cases (which includes `list:paired`, yay), it can only tag based on the element identifier of a child. It cannot tag the `p…
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Hi!
I'm wondering how to use the new GATK4 copy number segmentation as input to TITAN. I guess it should be possible (see eg. https://software.broadinstitute.org/gatk/documentation/article?id=11088…
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Clinical Significance should mention the new Oncogenic evidence type
>Positive or negative association of the Variant with predictive, prognostic, diagnostic, or predisposing evidence types. If the v…