User: altuna akalin

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Germany/Berlin/MDC-BIMSB
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http://bioinformatics....
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AltunaAkalin
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Last seen:
11 months ago
Joined:
4 years, 6 months ago
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Posts by altuna akalin

<prev • 12 results • page 1 of 2 • next >
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Answer: A: readTranscriptFeatures from genomation
... GFF to bed12 conversion doesn’t always work. Assuming it worked, you should just use provide the bed12 file path as the first argument to readTranscriptFeatures function Best Altuna Sent from mobile, excuse the brevity ...
written 21 days ago by altuna akalin20
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Comment: C: Error:no method for coercing this S4 class to a vector
... I updated the answer, I meant plotTargetAnnotation. Could you please let me know which part of the documentation is confusing, assuming you got the idea somewhere from the docs ? ...
written 11 months ago by altuna akalin20
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Comment: C: Error:no method for coercing this S4 class to a vector
... I updated the answer, I meant plotTargetAnnotation. Could you please let me know which part of the documentation is confusing, assuming you got the idea somewhere from the docs ? ...
written 11 months ago by altuna akalin20
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Answer: A: Error:no method for coercing this S4 class to a vector
... try using plotTargetAnnotation() ...
written 11 months ago by altuna akalin20
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Answer: A: normalizecoverage in methylkit outputs NAs
... Normalizing coverage shouldn’t lead to NAs. The thing that might lead to NAs is using ,min.per.group=3L In the unite function. Why this happens is explained in the docs, probably in the vignette and also in the discussion forum https://groups.google.com/forum/m/#!forum/methylkit_discussion If this ...
written 13 months ago by altuna akalin20
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Answer: A: Extracting gene structures from a GFF3 file for use with annotateWithGeneParts()
... I already answered this exact question here: https://groups.google.com/forum/#!topic/genomation/5EFpaBBEWLQ you can do that if you can create a GRanges list that has the same structure with readTranscriptFeatures() output. It returns a GRangesList most likely or simple list with GRanges (I think it ...
written 16 months ago by altuna akalin20
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Answer: A: MethylKit DSS Package
... Yes, this is because there are no replicates. calculateDiffMeth will run just the fisher’s exact test when there no replicates. That’s why it works when there are no replicates On Tue 17. Jul 2018 at 17:13, nilaycan [bioc] <noreply@bioconductor.org> wrote: > Activity on a post you are fo ...
written 17 months ago by altuna akalin20
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Answer: A: report error of methylkit
... can you try dbtype = NA and see if the problems persists? Please also make sure you are using the latest version. If you want further assistance please send a reproducible example, https://stackoverflow.com/questions/5963269/how-to- make-a-great-r-reproducible-example On Wed, Jul 5, 2017 at 8:36 A ...
written 2.4 years ago by altuna akalin20
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Answer: A: error reading bismark sam/bam files
... Try to update your R and BioC, and retry. Also have a look at the similar problems mentioned here: https://groups.google.com/forum/#!forum/methylkit_discussion On Fri, Jun 16, 2017 at 1:34 PM, kamal.fartiyal84 [bioc] < noreply@bioconductor.org> wrote: > Activity on a post you are followin ...
written 2.5 years ago by altuna akalin20
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Answer: A: Heatmap of motif clusters
... You can't show three different motif occurrence matrices on the same heatmap with different color codings for each motif using genomation. However, you can show those in three separate heatmaps. The problem with showing all three motif position sets in one heatmap is the positions where two or more ...
written 3.3 years ago by altuna akalin20

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Popular Question 3.3 years ago, created a question with more than 1,000 views. For Bioinformatics Scientist @ Berlin Institute for Medical Systems Biology

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