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Hi Gavin
I've been running the Titan snakemake workflow and would be grateful if you could clarify a few things for me:
1. In the optimalClusterSolution.txt file, what does the "...cluster_X_" a…
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@dinvlad @bistline @coreone @Puriney @eweitz @GeorgescuC
Hello inferCNV team,
I am running the inferCNC code and it runs properly, until I get the following error:
Computing nearest neighbor g…
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I would like to express my sincere congratulations on your recent publication titled "Evolution of immune and stromal cell states and ecotypes during gastric adenocarcinoma progression". Your outsta…
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Hi,
Thank you for developing this tool which is quite easy to use!
I am wondering if SpecHLA could also be used to detect somatic HLA mutations since we have paired tumor and normal WES or RNA…
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Hi,
Now I have normal vcf and tumor vcf produced by traditional lumpy seperately. To call genotype, should I:
(1) svtyper normal vcf and tumor vcf seperately?
(2) use bcftools merge the two vcf …
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When i run the code
directory_to_move = "PATIENT_DICOM"
desired_scans_path = os.path.join("train", "patients")
desired_masks_path = os.path.join("train", "masks")
try:
os.mkdir("train")
…
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Hi,
i try to understand how to run your workflow.
I launch this command on a cluster with cwlref-runner and cwltool installed:
```
cwl-runner tumor_heterogeneity_sciclone_based_workflow.cwl
```
…
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#### Summary
I have a test case for a 4bp indel where the allele frequencies and reported probabilities look wrong, while changing the allele to be just an SNV gives the correct results.
#### Deta…
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Hi!
I enjoyed the paper and am really interested in trying out the method. Would you be willing to write a short tutorial, or give some advice on which functions to use to perform imputation with …
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