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The article you published, "Deep learning predicts DNA methylation regulatory variants in the human brain and elucidates the genetics of psychiatric disorders," has been very helpful to me. However, u…
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Would it be possible to use LOLA to test for enrichment of significant individual CpGs identified in DNA methylation study? we can make a .bed file for each sig CpG, would that be ok to use as input f…
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Hello,
I have some DNA methylation data, which I prepared using EM-Seq and got around 236 million paired-end reads after sequencing on the Illumina NextSeq platform. I have some concerns regarding …
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Dear yupenghe,
Why DMR does not need to distinguish +/- strand like DMS ?
Thanks.
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Hi Prof. Xijin,
I am proposing to use iDEP for pathway analysis in a multi-omics model. We have RNA seq gene expression, DNA methylation and genetic variants SNPs data. I am wondering if I can use…
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Hi,
I have a question about your algorithm usage.
Your algorithm is a signal-based approach. When you translate the genomic region of interest into the expected signals by the k-mer pore model,…
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I work with the ESCA project, looking at Esophageal adenocarcinoma. However, TCGA has placed squamous cell alongside Adenocarcinoma, the diseases are significantly different leading to the immensely p…
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Hi Guo,
sorry to disturb you again, but I still have some questions. I used cgmapstat to obtain relative information with the rice.CGmap.gz as input. The result is as the picture show:
![cgmap](…
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Hi all,
These three new terms will be added to the ontology in order to allow curation of some types of RNA interactions and RNA/DNA-related features:
[Term]
id: MI:2201
name: DNA chemical modificat…
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d. h. tran, t. h. pham, k. satou, and t. b. ho, "conditionalrandom fields for predicting and analyzing histone occupancy,acetylation and methylation areas in dna sequences," lecturenotes in compu…