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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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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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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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`chr3 101703348 Minda_95 N . PASS SVLEN=3190;SVTYPE=DEL;SUPP_VEC=PB_ID_51866_2,PB_d_315,ONT_ID_11133_2,ONT_d_150,ILL_MantaDEL:64089:0:1:0:0:0,PB_severus_DEL4753,ONT_severus_DEL5502,PB_Sniffles2.DEL.2…
jzook updated
3 weeks ago
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- oncology is a broad therapeutic area - need to focus on sub-areas of oncology
- solid tumor - how quickly and how significantly you can shrink the tumor
- hematological - decrease/increase of para…
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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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When running PAMES::get_purity(beta) it seems to require normal samples beta values and the AUC-file. Is it possible to run it using only beta-values from the tumor sample?
Best,
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Hello,
I would like to use the pipeline to call somatic mutations from tumor-only RNAseq data. Would you mind to detail that how to generate the Panel of Normals?
Thanks,
Ya
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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…
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Hi All,
Maybe I missed something but are there a command in snakemake file to specify a sample-paired normal control in the snakemake file? I successfully run once in tumor only mode.
Thanks.