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Hello
What is meant by Normal Expression data? In cancer research we RNAseq tumor only usually
Thanks
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Currently, I have been using ichorCNA for cfDNA analysis in HCC. However, results of several patients showed that their tumor fraction equal to 0. Is there a theoretical threshold for ichorCNA detecti…
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We're currently only extracting gene acronyms (whether canonical or noncanonical), ensembl IDs and RefSeq IDs. In sentences such as the following:
`SDF-1 and CXC receptor 4 ( CXCR4 ) expression in rh…
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To assess the affects of tumor purity on our results, we should re-run certain survival models, considering only samples that have `tumor_fraction>= median tumor fraction` (https://github.com/AlexsLem…
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## Need
### TMB calculation today in BALSAMIC
The current definition is based on:
1. TMB was defined as the number of somatic, coding, base substitution, and indel mutations per megabase of genome …
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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…
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Hi,
Balsamic now creates '.CGH' files which is great. When I download the file it has both Starlims ID and Scout case number in the file name. However, when I open the file in cytosure it only says …
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Hi,
I am running the snakemake pipeline for TitanCNA for tumor/normals, where my maxploidy is set for 2 (that is what we believe of our sample) and I am doing different cluster initializations. I …
udp3f updated
4 years ago
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Hey cellchat team, thanks for the great package! I have analyzed my single cell datasets separately and now am trying to compare two conditions with the merge cell chat features. I am following the di…
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- [ ] #120
- [x] test set level table
- [x] gene level cancer type heatmap
- [x] patient specific bar graph stratified by cancer type
![image](https://github.com/jyaacoub/MutDTA/assets/50300488/…