User: Mike

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Mike1.3k
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Location:
UK
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Joined:
3 years, 3 months ago
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Posts by Mike

<prev • 210 results • page 1 of 21 • next >
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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 18 days ago by Mike1.3k • updated 16 days ago by Martina10
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Comment: C: Who are the Greatest Bioinformaticians Of All Time (GBOAT)
... Good list Kevin, No. 6: Biostars.org's unsung heroes (Pierre Lindenbaum, Devon Ryan, Istvan Albert, genomax , Michael Dondrup , Kevin Blighe, WouterDeCoster, Alex Reynolds, Giovanni M Dall'Olio, Sean Davis , Emily_Ensembl etc) ...
written 10 weeks ago by Mike1.3k
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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 11 weeks 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 11 weeks 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 11 weeks 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 11 weeks ago by Mike1.3k
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Comment: C: TCGA survival analysis: continuous vs discrete expression values
... Thanks again, yes there is difference in HRs with confidence intervals (upper/lower 95) HR HRlower HRupper 0.82 0.770 1.01 (discrete) 0.87 0.75 0.97 (continues) ...
written 4 months ago by Mike1.3k
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Comment: C: TCGA survival analysis: continuous vs discrete expression values
... Thanks Kevin for your help, I found a relevant article on this issue. Comparing continuous and discrete analyses of breast cancer survival information https://www.sciencedirect.com/science/article/pii/S0888754316300684 ...
written 4 months ago by Mike1.3k
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Comment: C: TCGA survival analysis: continuous vs discrete expression values
... nearly the same results using Z-scores data for discrete (logrankP= 0.02 ) & continuous model (logrankP= 0.00004 ). ...
written 4 months ago by Mike1.3k
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Comment: C: TCGA survival analysis: continuous vs discrete expression values
... Thanks Kevin, expression data is RSEM log2 and this is distribution. https://ibb.co/pbWBV0g Median expresssion values of this gene is 8.73 in 452 samples ...
written 4 months ago by Mike1.3k

Latest awards to Mike

Scholar 18 days ago, created an answer that has been accepted. For A: survival analysis question
Teacher 18 days ago, created an answer with at least 3 up-votes. For C: Starting a career in Bioinformatics
Great Question 10 weeks ago, created a question with more than 5,000 views. For Single Cell RNAseq data analysis protocol
Popular Question 10 weeks ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Commentator 10 weeks ago, created a comment with at least 3 up-votes. For A: Protocol to Downlad TCGA data from GDC
Popular Question 3 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Great Question 3 months ago, created a question with more than 5,000 views. For Single Cell RNAseq data analysis protocol
Popular Question 3 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
Popular Question 5 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Good Question 6 months ago, asked a question that was upvoted at least 5 times. For Single Cell RNAseq data analysis protocol
Appreciated 9 months ago, created a post with more than 5 votes. For A: Single Cell RNAseq data analysis protocol
Popular Question 9 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Good Question 9 months ago, asked a question that was upvoted at least 5 times. For Single Cell RNAseq data analysis protocol
Scholar 10 months ago, created an answer that has been accepted. For A: survival analysis question
Guru 10 months ago, received more than 100 upvotes.
Popular Question 11 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
Popular Question 11 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Popular Question 14 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Popular Question 14 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
Popular Question 16 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Popular Question 17 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Popular Question 18 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format
Popular Question 19 months ago, created a question with more than 1,000 views. For TCGA data: comparision in normal and tumor samples
Popular Question 19 months ago, created a question with more than 1,000 views. For GSEA with TCGA data
Popular Question 19 months ago, created a question with more than 1,000 views. For clusterProfiler: Input file format

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