User: e.rempel

gravatar for e.rempel
e.rempel200
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200
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Location:
Germany, Heidelberg, COS
Last seen:
2 hours ago
Joined:
2 years, 3 months ago
Email:
e*******@dkfz-heidelberg.de

Posts by e.rempel

<prev • 25 results • page 1 of 3 • next >
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Answer: A: input of cummerbund
... Hi, there is a button in Galaxy UI "Generate SQLite" (default is "NO" !) for **CuffDiff** tool. Select "Yes", then CuffDiff will generate a SQLite output ready to be used as an only input for CummerBund. ...
written 11 days ago by e.rempel200
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Answer: A: Heatmap.2 giving specific color to a value and start gradient after
... Hi Seigfried, you give the separate colors, but **ColorRamPalette** still interpolates them to create a smooth gradient from white to yellow to orange to red. If I understood you correctly, you would like first create a smooth gradient from yellow to orange to red and **then** prepend "white". Thu ...
written 13 days ago by e.rempel200
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Answer: A: Combining viral and host GTF files
... Hi, I think you could just add the viral GTF to the human assuming the chromosome identifiers don't overlap. ...
written 15 days ago by e.rempel200
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Comment: C: heatmap.2 reorder branches
... Sorry to hear that. I had always to experiment with the weights to get the order of branches I want. Maybe it is worth trying different agglo.FUN in *reorder* (e.g. *mean* or *max*)? ...
written 23 days ago by e.rempel200
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Comment: C: heatmap.2 reorder branches
... Hi b.note, I assume it doesn't work since *reorder* (or actually *reorder.dendrogram*) agglomerate node weights to obtain "weights" of branches/subtrees. Per default, agglomeration function summarizes the weights, thus to put a specific branch before the others, you might need to assign a very high ...
written 23 days ago by e.rempel200
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Answer: A: How to calculate GOsimilarity between different species
... Hi, you could actually use **GOSemSim** package to calculate semantic similarity of two groups of GO terms, whereby the groups could be from different species. For this purpose, you could use the function *mgoSim* ...
written 8 weeks ago by e.rempel200
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Answer: A: Gene list from bed file
... Hi, you also can use [bedtools intersect][1]. From the online manual: > bedtools intersect allows one to screen for overlaps between two sets of genomic features. One set is your bed file, the second file could be a GFF/GTF file with the gene model of your organism. [1]: http://bedtools.rea ...
written 9 weeks ago by e.rempel200
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Comment: C: Calculating p-Value for an observed/expected Ratio
... A small comment on this excellent answer. Do you expect reads to come from entire genome (since you are shuffling over it)? Maybe it is worth thinking to restrict it to the open chromatin regions. ...
written 9 weeks ago by e.rempel200
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Comment: C: clustering cell population in different phenotypes
... Personally, I would like to use all biological replicates. On a side note: have you run K-means clustering multiple times since it is a randomized algorithm? ...
written 9 weeks ago by e.rempel200
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Comment: C: clustering cell population in different phenotypes
... Hi, additional question: expression of how many genes do you have? The reason I am asking is this: if you have expression data of many genes it makes sometimes sense to preselect genes before K-means clustering (**Feature selection**) ...
written 9 weeks ago by e.rempel200

Latest awards to e.rempel

Appreciated 12 weeks ago, created a post with more than 5 votes. For A: GO analysis using topGO Arabidopsis
Scholar 12 weeks ago, created an answer that has been accepted. For A: GO analysis using topGO Arabidopsis
Teacher 12 weeks ago, created an answer with at least 3 up-votes. For A: GO analysis using topGO Arabidopsis

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