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It sounds like we are currently using raw beta values from the array probe that is most negatively correlated with expression.
For comparison, the mRNA expression data that we provide has gone thro…
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From TCGA, this data is our prediction input.
Information Needed
- Source of data
- Where data is located
- Description of data
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I did a benchmark over the 2 imputation methods over following procedure
1. Run a small imputation benchmark on KNN and softImpute(SVD)
1. subset the first 10,000 of the CpG sites with totally …
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Hi Levi and Marcel,
I was wondering if it would be possible to implement a simplified methylation data set. As you know the raw methylation data is quite unwieldy so I condensed it to a matrix, whe…
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Hi Felix,
I have two questions.
1) I managed to get my COV files uploaded onto Seqmonk and got to visualizing the probes using 'Bisulphite Methylation Over' pipeline but I haven't been able to …
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Hi Art,
I'm trying to call methylation sites in the ecoli test data but there are no results in the output directory. I took out the --twoWay flag, since it was causing an error (& deprecated in favo…
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Hi,
I am working with WGBS data on a non-model organism. I used Bismark (with Bowtie) to align my reads and would like to use Methylpy to identify DMRs. I installed methylpy in a conda environment…
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Dear Peng,
I wonder if it is possible to use Deepsignal to detect methylations in RNA from samples sequenced by the direct RNA sequencing kit from ONT.
I think about training a model by using comp…
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Hi,
I have generated human genome based methylation call output for a sample using Modkit pileup command.
The output bedmethyl file has following data, where for position 10566 both 5hmC and 5mC are…
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Thank you for this very useful tool! I have been trying to use MethylDackel to analyze data acquired from a NOMe-seq type method, in which GpC methylation (in addition to CpG methylation) is an inform…