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**Content team**
Page one - tumor level:
- [ ] spatial plots color coding points by positivity
- [ ] summary plots of distributions of markers
- [x] ripleys K plots (along various values of R…
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### Description of the bug
As seen in the attached log file, the pipeline stops working and cycles in error with amazonaws. I am new to nf-core so I am unfamiliar with how all the parts of the pipeli…
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**Implementation:**
Based on discussions with MOHCCN Clinical Commitee and ARGO CMD Working Group, the following two new optional fields will be added to the Radiation schema:
| Field Name | Des…
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Hi, I want to train GMS model with msd pancreas dataset. And it has 3 classes(background, pancreas, tumor).
How can I train those 3 classes with your code? I don't know which variable indicates the n…
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This is because the human gene has a preferred label of `tp53`, while the mouse gene has a preferred label of `trp53`. It is therefore being sorted below all the other genes that have a preferred labe…
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Hi ,
I have a normal and tumor bam file from patient sample.I would like to view the micro satellites in the sample.I tried scanning reference genome hg38 and hg19 from ucsc genome browser.
I can cr…
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Hello! I am very inspired by your work. Referring to your work, I have some doubts while pre-training MRI data.
I want to use brain tumor MRI containing four modalities for pre-training, what to do …
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Hi!
I have WES with ~30x coverage, matched normal-tumor samples and I am interested in somatic mutations. Unfortunately, it is not clear for me, what kind of vcf file should I use as an input for snp…
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### Description of the bug
When the "sampleID" in the samplesheet is not unique, only the output files for the final patient are kept. For example the following samplesheet would only keep the outout…
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Morphology is defined as an element of bodyStructure (see https://build.fhir.org/bodystructure.html) but, I assume, we don't want to put diagnosis in the bodyStructure element. Therefore we came acros…