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Hi, first of all thank you for the amazing work and codebase. I see that the data folds for the subtype classification task are provided in HIPT/2-Weakly-Supervised-Subtyping/splits/10foldcv_subtype.
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https://mp.weixin.qq.com/s/ZdryruwRXqBgOQTayfFF4g
ixxmu updated
6 months ago
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I have been working with the TCGA slides for my project.
As the first process, I have created patches using `create_patches_fp.py` script for the custom threshold parameters. The problem is that it …
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https://mp.weixin.qq.com/s/kqpoA_Brbbt88GZnc38S2w
ixxmu updated
6 months ago
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Hi,
When I used svaba to run in germline mode, with the following command:
~/tools/svaba run -t ../../../2.bam -k k.bed -a RT -L 6 -I -p 10 -G ssc11_1.fa
the log file reminds:
Running region 1:1…
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Thanks for your great work, sorry to bother you. Since you have uploaded the filenames and the labels of [CAM16 dataset](https://github.com/DearCaat/MHIM-MIL/blob/master/label.csv), could you also pl…
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# Summary
Attempting to `subset` a `SeuratObject` after adding a spatial coordinates layer (via. `Seurat.object[["example"]]
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I encountered an issue when using `GDCprepare` from` TCGAbiolinks version 2.30.0` to retrieve Simple Nucleotide Variation data for `TCGA-CESC`. The error message is as follows:
```
dplyr::bind_rows(…
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I need the versions of the cache for VEP and SNPEFF that correspond to ensembl release 102. This is relevant for all of us that use TCGA data as that is what they use. When I run:
`nextflow run nf-…
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Looking forward to the author's answer, thanks!