User: Mike
Mike • 1.5k
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Posts by Mike
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... rMATS is for detect differential alternative splicing events. ...
written 7 months ago by
Mike • 1.5k
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... I am looking for mutually exclusive expressed genes ...
written 7 months ago by
Mike • 1.5k
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... Hi everyone,
I want to check how some of my interesting genes are statistical significantly mutually exclusive expressed in BRCA-TCGA expression data.
Does anyone know how to do this?
Thanks ...
written 7 months ago by
Mike • 1.5k
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... Nice explanation thank you so much,
So number in count matrix is "number of Tn5 insertions" , If this number is high then peak height also would be high and this is probability for open chromatin structure. Am I right ? Can I use this numbers to find differential significant peaks between two class ...
written 8 months ago by
Mike • 1.5k
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... Hi all,
I am using TCGA ATAC data (bigwig files) to visualizing some peaks for some genes. In this paper there is a normalised count matrix file for each peak and sample? In supplementary file they mentioned that “To get the number of Tn5 insertions per peak, each corrected insertion site (end of a ...
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... Hi All,
I have TCGA MAF files and want to calculate base substitution mutation frequency (C>T , T>A , C>G , T>C , T>G , C>A) per sample. If anyone knows please help me ?
Thanks ...
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... Thanks Kevin and bruce.moran for your help ...
written 12 months ago by
Mike • 1.5k
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... Thanks you so much Kevin, I also found a paper where they mentioned that..
> we calculated the TMB score as follows:
>
> total number of truncating mutations*1.5 + total number of non-truncating mutations*1.0.
Truncating mutations included nonsense, frame-shift deletion, frame-shift ...
written 12 months ago by
Mike • 1.5k
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... Thanks bruce.moran, I have TCGA MAF files (Mutation_Packager_Raw_Calls) downloaded from Broad Institute Firehose. ...
written 12 months ago by
Mike • 1.5k
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... Hi All,
What is difference between "Tumor Mutation Burden (TMB)" and "mutational load" ? I have mutation matrix for TCGA samples (generated from maftools, see below). I tried maftools and GenVisR but couldn't find any option to calculate TMB score. How can I calculate TMB score using mutation mat ...
written 12 months ago by
Mike • 1.5k
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