User: kuckunniwid

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kuckunniwid20
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Posts by kuckunniwid

<prev • 27 results • page 1 of 3 • next >
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Pathway Annotation, grouping of sparse data on pathway level
... I am sorry if this question is a duplicate - I could not find anything that match exactly this, I am trying to find genomic differences between two conditions (response to therapy). And I was not able to find a difference on gene level (cohort size is not that big, each gene is affected only in cou ...
pathway written 3 days ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... thanks a lot! by permutations I means "calculate differences between normal and tumor and premute them across the genome to calculate pvalues for non-permuted data", but I guess it is not required taking into account your comprehensive answer. Thanks a lot, will try thes approaches! COHCAP looks lik ...
written 12 weeks ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... Thank you a lot for such a comprehensive answer! I have one question more. I have paired samples, normal and tumor. How would you proceed with such data? Is adding information about pairing as contrast matrix enough, or should I manipulate with the data itself (eg. working with differences in methyl ...
written 12 weeks ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... Wow, I've used metilene, but never thought that it can work with more than 2 groups (and it actually is). Thanks! Will try it. Ah no, looks like "multiple" groups for them means 2 - http://www.bioinf.uni-leipzig.de/Software/metilene/Start/ ...
written 12 weeks ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... Absolutely. I can reveal the design, but I am not sure if it will be helpful. The problem with significance is - I use dmrseq and, even if I have 1MB long stretch when the groups are almost perfectly separated with the visible effect, the q-value is like 0.2. This tool uses honest permutation approa ...
written 12 weeks ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... which is totally true, so a person who is looking for paired DMR methylation caller will be able to find this question and probably get useful information. ...
written 12 weeks ago by kuckunniwid20
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Comment: C: Paired DMR methylation caller
... I mean, if a person does not know what DMR is - he will not be able to help me, no? It is a differentially methylated region. Have no idea what MMD is. ...
written 12 weeks ago by kuckunniwid20 • updated 12 weeks ago by Michael Dondrup45k
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Paired DMR methylation caller
... Hi, I am looking for a tool that can detect DMRs using the pairing information from normal-tumor samples. Looks like my study is kind of underpowered (because nobody asked me about the study design) and the only way to improve the power is to use all prior information. Do you know such callers? Rea ...
dmr bisulfite written 12 weeks ago by kuckunniwid20 • updated 12 weeks ago by Charles Warden6.1k
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Visualize B-allele frequency on IGV for 2 samples
... Dear All, I have a non-standard task - visualize B-allele frequency tracks for 2 samples in 1 track in IGV. It is not difficult to make it for each sample separately using basic IGV format: #type=GENE_EXPRESSION #track graphtype=points name="Sample1.igv" color=0,0,255 altColor=255,0,0 maxH ...
file-format igv written 3 months ago by kuckunniwid20
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Answer: A: Enrichment platforms for 1000GP exome data
... The answer is actually here: http://www.internationalgenome.org/category/exome/ ...
written 4 months ago by kuckunniwid20

Latest awards to kuckunniwid

Scholar 14 months ago, created an answer that has been accepted. For A: Inconsistent Coverage on X chromosome between genders
Teacher 14 months ago, created an answer with at least 3 up-votes. For A: Inconsistent Coverage on X chromosome between genders

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