methylKit
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al2na
R package for DNA methylation analysis
Hello I m using methylkit on bismark alignment files. I used the command below and used the bam output from bismark alignment process: `methRaw = processBismarkAln( location = "/media/genome2/SP PHD...
Hello, I apologize in advance as I am relatively new to bioinformatics. I attempted to use your tool to extract the most differentially methylated genes, but I am encountering a...
Hello @alexg9010 . I do have an unbalanced number of replicates for my conditions. For example, one condition A has 5 replicates B - 3 and C - 4. Can...
I am trying the unite large samples after filtering its seem fine, but after unite chromosome and strand column are showing meta character instead of name chr start end strand...
Hello Alex, I have a small question about RRBS methylation data. It is my question that I post before. My question this time is how to use RRBS methylation data...
Hi! I am analysing methylation data with methylKit on R and I got some NA values after the unite function, after merging samples: meth=unite(myobj, destrand=FALSE) This issue does not allow...
Hello, I do have a question regarding the feature strand if its + or -, and how to consider each relative to the TSS. Thank you > tss_assoc_hyper target.row dist.to.feature...
Hi, I have the error shown in the title. It was thown by tabix2dt in chrY_JH584300_random, in which I used applyTbxByChr to read methDiffDB, because in WGBS it met core...
by checking for existing `dbtype` https://github.com/al2na/methylKit/blob/ecf85842bdd5252161fa5bbe6aa0d285c87e1f77/R/tabix.functions.R#L355
The output file is currently assumed in the same folder as the input tabix file. This is violated if `dbdir` argument is given. The file is created at the correct...