User: kwanghoon

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kwanghoon10
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1 week ago
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4 months, 3 weeks ago
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k********@snu.ac.kr

Posts by kwanghoon

<prev • 16 results • page 1 of 2 • next >
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Methylation data analysis using unsupervised hierarchical clustering
... Hi there. I have some methylation array data (EPIC 850k) and I'm trying to analyse these data by using unsupervised hierarchical clustering. Is there any tutorial? https://www.datacamp.com/community/tutorials/hierarchical-clustering-R I found this site, should I start with beta values of methylat ...
epic methylation array written 9 days ago by kwanghoon10
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What statistical method do I have to use to see expression tendency?
... Hi, I'm trying to see RNA expression tendency of 'some genes' when 'A gene' increases. I draw linear regression but I doubt that I'm doing right. Is there any method? Sorry for bad explanation. ...
statstics tcga expression written 7 weeks ago by kwanghoon10
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Comment: C: Does anyone have experience of methylation alignment tool "Bismark"?
... yeah I saw that docs too. I was not sure about that so I made question. Anyway thank you! ...
written 10 weeks ago by kwanghoon10
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Does anyone have experience of methylation alignment tool "Bismark"?
... Hi, I'm trying to align my methylation data using Bismark I did something.... so I got .bam file. I converted it to .sam to see how it looks like. I saw weird thing(sequence?) like K00171:752:HW5LHBBXX:4:1207:3082:33457_1:N:0:CGACACAC 83 chr1 10003 6 101M = 10009 -10 ...
ngs methylation bismark written 11 weeks ago by kwanghoon10 • updated 11 weeks ago by MatthewP730
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Comment: C: About hg38 reference genome indexing
... Thank you now I can understand..! ...
written 11 weeks ago by kwanghoon10
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About hg38 reference genome indexing
... Hi I tried to index reference genome fasta (hg38) that I downloaded UCSC version from below https://www.gungorbudak.com/blog/2018/05/16/how-to-download-hg38-grch38-fasta-human-reference-genome/ Used bwa, samtools(.fa.fai), picard(.dict) Commands are bwa index -a bwtsw hg38.fa samtools faidx hg ...
hg38 reference genome written 11 weeks ago by kwanghoon10
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How do I analyze MGMT methylation status from EPIC array data?
... Hi, I have data generated by using EPIC array(850k) I'm trying to check MGMT methylation status from these brain tumor data. I tried to download R package "mgmtstp27" but installation kept failed. (Some papers used this package, so I also tried) https://github.com/badozor/mgmtstp27 ---------- &g ...
mgmt epic array methylation brain tumor written 3 months ago by kwanghoon10
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dbSNP rs number
... Hi, I downloaded annotated-mutation information from TCGA-GBM (mutect2). I found some dbSNP_RS is NA and novel. Should I remove these mutations? ...
tcga dbsnp written 3 months ago by kwanghoon10
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Comment: C: GEO raw data download
... Thank you again Kevin! I downloaded raw files using R package 'GEOquery' using getGEOSuppFiles() command. (Also takes some time, but faster than download link :) ) And As you recommended, I found beta value and detection p-value :) Thank you! ...
written 3 months ago by kwanghoon10
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GEO raw data download
... Hi I'm trying to download Supplementary file(GSE109381_RAW.tar) at https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE109381 I clicked "http" link, but it will take 2 days... Is there any other way to download this?(in R, python something) Thank you. ...
geo methylation written 3 months ago by kwanghoon10 • updated 3 months ago by Kevin Blighe65k

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