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Dear authors,
First, I want to applaud you for your great paper acceptance, and thank you for making the model weights available. I read your paper carefully, but I still have questions I hope you …
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Hello,
Thanks for this useful utility.
I have data in MAF format (NCBI build 37). I am trying to lift it over to hg38 using the following Crossmap (v0.6.6) command:
```
CrossMap maf b37ToHg38.…
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Apologies this is a long post about this Nature article, I have been reading the paper since it come out and I have MANY questions, too many to list in a single post. For some context I have been clos…
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Dear authors,
What is pretraining distribution of CTransPath and CHIEF? Is new CHIEF CTransPath model the same as previous one in Medical Image Analysis?
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I am running the "case studies" from this page "https://bioconductor.org/packages/release/bioc/vignettes/TCGAbiolinks/inst/doc/casestudy.html"
and I find error information like below:
> TabCoxNe…
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I worked a bit on the labelling matching with ENA / NCBI as I had a lot of mismatch issues with the development of the FAIR Data Station. I forked the repo and did an analysis on the terms in MIxS and…
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How would someone extract the schema specific data needed in order to populate lists of all of the possible values for the pathological, and clinical values for the T, N, M, and Stage Group fields? S…
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Dear authors,
I have read your paper and still do not have deep understanding of how to pretrain CHIEF model. My confusion is in pretraining method and want to discuss this method.
- I wish to v…
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- [ ] Review the high level classification of ‘cancer or benign tumor’ and ‘neoplastic disease or syndrome’ and ensure the classifications make sense
- [ ] make cancer and predisposition to cancer di…
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(note: [this was crossposted at BioStars](https://www.biostars.org/p/234435/))
I am retrieving and parsing some data from GDC using TCGAbiolinks:
```
library(TCGAbiolinks)
patientdownload