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Methylation Analysis EPIC array

methylation dmrcate gene expression minfi written 18 days ago by Will Yam • 0

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2.5k

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7 follow

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DMRcate results: How to find out which CpG sites constitute each DMR

R bioconductor methylation dmrcate written 2.9 years ago by c.ryder3 • 30 • updated 8 months ago by 123456789 • 0

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392

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DMRcate: How to get Cpgids present in the DMR

dmrcate cpgids methylation epicarray written 9 months ago by bassanio • 20

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339

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DMRcate results: How to interpret the overlapping.promoters

dna methylation dmrcate R champ written 10 months ago by sugus • 50

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614

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DMR.plot Erreur : Bad Request

R dmrcate dna methylation written 2.5 years ago by daron.6 • 0

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1.2k

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How to create a design matrix for Cpg.annotate?

R bioconductor dmrcate cpg.annotate written 2.9 years ago by c.ryder3 • 30 • updated 2.9 years ago by e.rempel • 890

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A workflow for identification of differentially methylated regions, starting with a data frame of beta values?

450k R bioconductor methylation dmrcate written 2.9 years ago by c.ryder3 • 30 • updated 2.9 years ago by halo22 • 150

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categorize DMRs by type (hyper - hypo methilated) in DMRcate or minfi

450k dmrcate hypo mehylated minfi hyper methylated written 3.2 years ago by rahel14350 • 30

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1.1k

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visualization of DMRcate or minfi output on UCSC

450k dmrcate track hub minfi ucsc written 3.2 years ago by rahel14350 • 30 • updated 3.2 years ago by asyavuz • 130

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Recent Replies

C: Comparing GISTIC2 G-Scores in matched samples by noodle • 30
Yep, apologies, these values are already logged. ol.gr$diff_gscore <- ol.gr$mets_G_Sc...
C: VCF tools --freq output file by Inquisitive8995 • 160
Hi, Thanks for your reply. If I go by the calculation, can I confidently say that the first colum...
A: How to extract ~2M short sequences based on coordinates from a 3G fasta file? by kynnjo • 20
Shortly after I posted this question I found that samtools faidx -r ... does what I need.
A: Removal of primers from matched sequences by Joe ♦ 17k
The data structure you have is pretty confusing and heavily nested, but I *think* this is correct...
C: How to extract reads that map with BWA exactly twice by genomax ♦ 85k
But are you able to see > multi-map reads which map twice, once to the father and once to th...
C: Removal of primers from matched sequences by cpad0112 ♦ 13k
try cutadapt
C: Why Salmon produces different quantification results compared with featureCounts by biock • 30
Thank you. I run featureCounts on your advice but I found the correlation didn't change a lot com...
A: How to extract reads that map with BWA exactly twice by thomashartwig80 • 0
Hi. We are using BWA-mem (now BWA-mem2). Using a diploid genome was the only way to truly elimina...
C: Comparing GISTIC2 G-Scores in matched samples by Kevin Blighe ♦ 61k
Great that you got it working, but I would definitely 'spot check' the end result just to make su...
C: Comparing GISTIC2 G-Scores in matched samples by noodle • 30
In terms of calculating the difference in G scores at overlapping regions, does taking the log2 ...
C: Comparing GISTIC2 G-Scores in matched samples by noodle • 30
Okies, i think I have it figured out- thanks Kevin! 2 heads are definitely better than 1 # f...
A: Linkage_pruning in BCFtools+prune:phased or unphased VCF input file? by Aremkh • 10
In case you have the same question, please refer to the answer at: https://github.com/samtools/bc...

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