-
Hello, I'm currently using BayesPrism for deconvolution and I have a question.
I'm working with single-cell sequencing data, which includes an equal amount of tumor cells and normal (non-tumor) cel…
-
![image](https://github.com/jyaacoub/MutDTA/assets/50300488/e8b08281-bf79-429c-925d-0d385d736ffe)
## Test set level table
- count num mutations/gene (FOR TEST SET)
- then get stats on:
- t…
-
### Description of the bug
Hello, I am a newbie to nf-core sarek and I am running it on WES data for tumor-only, using CNVkit tool. Even though the pipeline completes successfully, the CNVkit tool …
-
Thanks for the great work.
You mentioned that location selection is the first step in tumor generation but I wonder where to find the code for it.
I noticed that random location is selected in `Tum…
-
## 🐛 Bug
I am unable to visualize intersections between more than 5 groups/samples using vis() on pubRepStatistics(). I have 13 groups but vis() only displays 5.
## To Reproduce
Steps to reprod…
-
### 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…
-
Hello,
We are trying to convert a brain tumor dataset into the bids format. This dataset has DSC perfusion mris. However, in the bids documentation I only found an equivalent for asl perfusion mri…
-
I have run decontam on a data set that has ASV’s for tumor tissue, negative controls, and control tissue. The negative controls did not have any tissue but only reagent. The controls are non-tumor spe…
-
Survival analysis (Cox regression and ggforest plot)
- 25 different tumors and no cancers
- PTV burden as a continuous variable
- Variables in the Cox models: sex, ethnic group, PCA1-10, PTV burd…
-
I would like to ask if its possible to select only Tumor-Normal paired samples or Tumor-Metastatic?