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### Need
MSI analysis was requested to be included to the workflow in https://github.com/Clinical-Genomics/BALSAMIC/issues/972
### Suggested approach
Add [MSIsensor-pro](https://github.com/x…
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Hello,
I have read your article "PreMSlm: An R package for predicting microsatellite instability from the expression profiling of a gene panel in
cancer". It is a nice tool for MSI prediction using …
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- [x] BAM Generation and Quality Control : ACCESS_pipeline.cwl (ACCESS-Pipeline/workflows/)
- [ ] Small Variants: snps_and_indels.cwl (ACCESS-Pipeline/workflows/subworkflows/)
- [x] Copy Number Vari…
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### Description
As a user, I want to understand the usability of models based on additional markers, such as
tumor mutational burden (TMB)
The total number of mutations (changes) found in the DNA of…
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The drug bank data needs to be examined and solutions developed for the extraction of meaningful terms and data regarding indications to help with the AMP/ASCO Tiering evaluation.
Values:
_Cancer ty…
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Hello!In training.py,a method named as cv_pic_list() is used to split datasets but not provided.So I implemented the code referring to the method with the same name in Pretrain.py.I mixed up all tiles…
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Hi,
I have some problems with MANTIS. I can't finish the process. I used WGS data (70 Gb - normal and 150 Gb - tumor) and 3 mln rows of loci bed basing on hg38 genome.
Also I used only chr16 fro…
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Hi,
I got following error:
`
Microsatellite Analysis for Normal-Tumor InStability (v1.0.3)
python /gpfs/gsfs6/users/MoCha/patidarr/MANTIS/kmer_repeat_counter.py \
-b /data/MoCha/patidarr/MANTIS/l…
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Hi, I have some questions while using the msisensor2, the description is "msi high: msi score >= 20%” in the offficial website (http://niulab.scgrid.cn/msisensor2/#services), while I also found that …
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- [x] Write script that generates folder structure to run the access pipeline.
This should consist of the following:
1. Given a project, create the project folder if it exists skip it.
2. …