User: Mike

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Mike1.3k
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Posts by Mike

<prev • 214 results • page 1 of 22 • next >
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Comment: C: How to find significantly mutually exclusive expressed genes in TCGA
... rMATS is for detect differential alternative splicing events. ...
written 13 days ago by Mike1.3k
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Comment: C: How to find significantly mutually exclusive expressed genes in TCGA
... I am looking for mutually exclusive expressed genes ...
written 13 days ago by Mike1.3k
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How to find significantly mutually exclusive expressed genes in TCGA
... 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 ...
correlation rna-seq mutual expression written 13 days ago by Mike1.3k
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Comment: C: Number of Tn5 insertions in TCGA ATAC-Seq data
... 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 6 weeks ago by Mike1.3k
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Number of Tn5 insertions in TCGA ATAC-Seq data
... 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 ...
tcga atac-seq sequencing written 6 weeks ago by Mike1.3k • updated 6 weeks ago by ATpoint23k
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How to calculate base substitution mutation frequency (C>T T>A C>G T>C T>G C>A) from TCGA MAF files
... 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 ...
maf tcga snp written 3 months ago by Mike1.3k • updated 3 months ago by Martina10
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Comment: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... Thanks Kevin and bruce.moran for your help ...
written 5 months ago by Mike1.3k
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Comment: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... 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 5 months ago by Mike1.3k
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Comment: C: How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... Thanks bruce.moran, I have TCGA MAF files (Mutation_Packager_Raw_Calls) downloaded from Broad Institute Firehose. ...
written 5 months ago by Mike1.3k
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How to calculate Tumor Mutation Burden (TMB) for TCGA samples
... 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 ...
genvisr tcga maftools tumor mutation burden tmb written 5 months ago by Mike1.3k

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Popular Question 3 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Scholar 3 months ago, created an answer that has been accepted. For A: survival analysis question
Teacher 3 months ago, created an answer with at least 3 up-votes. For C: Starting a career in Bioinformatics
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Great Question 7 months ago, created a question with more than 5,000 views. For Single Cell RNAseq data analysis protocol
Popular Question 7 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
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Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Single Cell RNAseq data analysis protocol
Good Question 12 months ago, asked a question that was upvoted at least 5 times. For Single Cell RNAseq data analysis protocol
Appreciated 12 months ago, created a post with more than 5 votes. For A: Single Cell RNAseq data analysis protocol
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Scholar 13 months ago, created an answer that has been accepted. For A: survival analysis question
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Popular Question 14 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
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