User: mbk0asis

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mbk0asis190
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Korea, Republic Of
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Posts by mbk0asis

<prev • 76 results • page 1 of 8 • next >
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Comment: C: How to calculate polygenic hazard score (PHS)?
... Thanks! I have been studying this paper but haven't figure out how to calculate that. Would you explain this in simple English or find a equation or something? It is too difficult to understand for a non-native English speaker who has no statistical background. Thank you! ...
written 2 hours ago by mbk0asis190
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Answer: A: select DE genes
... If all of your samples have the same phenotype (cancer for example), why would you want to find DEGs? You should have at least one control sample to compare with. Or you want to see the overall expression pattern of your data? In that case, you are going to need a lot of computer power. Data wi ...
written 4 days ago by mbk0asis190
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Answer: A: extract DP of heterozygotes from vcf file
... try grep -Po 'DP=.*' INPUT | cut -d";" -f1 INPUT chrX 129 . G GT,GGT 27173.73 . AC=1,1;AF=0.500,0.500;AN=2;BaseQRankSum=2.721;ClippingRankSum=-0.400;DP=2555;ExcessHet=3.0103;FS=0.000;MLEAC=1,1;MLEAF=0.500,0.500;MQ=40.46;MQRankSum=-3.139;QD=27.54;ReadPosRankSum=-1.613;SOR=2.163 GT:AD:DP:G ...
written 4 days ago by mbk0asis190
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Answer: A: Download data from TCGA
... 1. Go to [GDC data portal][1] 2. Click 'Data' 3. Select types of cancer and files (RNA-seq in your case) 4. Click 'Download Manifest' and save the manifest file. 5. Install 'GDC data transfer tool (gdc-client)'. 6. Go to the directory containing the manifest file. 7. In terminal (command line) ...
written 4 days ago by mbk0asis190
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Comment: C: select DE genes
... DEGs between individual patients or groups (cancer vs normal)? ...
written 4 days ago by mbk0asis190
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Comment: C: NGS data analysis
... 'vlookup' in MS Excel might work for you. ...
written 4 days ago by mbk0asis190
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How to calculate polygenic hazard score (PHS)?
... Hi. A recently published paper in [PLOS medicine][1] reported that they had developed a polygenic hazard score (PHS) for quantifying individual differences in age-specific genetic risk for Alzheimer disease (AD) with hazard ratios of disease associated 33 SNPs. Later in that paper, they predicted ...
alzheimer plygenic hazard score statistics written 14 days ago by mbk0asis190 • updated 14 days ago by anp37580
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TCGAbiolinks - GDCdownload error
... Hi. I'm trying to download TCGA DNA methylation data using 'GDCdownload' in 'TCGAbiolinks', but I'm getting this error message. > GDCdownload(query) GDCdownload will download 5201 files. A total of 110.697216048 GB Downloading as: Tue_Apr_11_09_28_55_2017.tar.gz |============= ...
tcgabiolinks gdcdownload written 14 days ago by mbk0asis190
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Comment: C: Memory allocation problems in 450k analysis
... What's the max sample size with 512G memory to run the analyses you mentioned? ...
written 5 weeks ago by mbk0asis190
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Comment: C: deepTools cluster information?
... Thank you! I missed that one... ...
written 10 weeks ago by mbk0asis190

Latest awards to mbk0asis

Popular Question 5 weeks ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Great Question 10 weeks ago, created a question with more than 5,000 views. For Finding a sequence in a fasta file
Popular Question 10 weeks ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 3 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 5 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file
Popular Question 8 months ago, created a question with more than 1,000 views. For Pairwise2 - Biopython - weird local alignment results
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Popular Question 19 months ago, created a question with more than 1,000 views. For Finding a sequence in a fasta file

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