User: e.rempel
e.rempel • 200
- Reputation:
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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
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2
votes
1
answer
112
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1
answers
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.rempel • 200
0
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3
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143
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answers
... 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.rempel • 200
2
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2
answers
130
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... 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.rempel • 200
0
votes
3
answers
478
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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.rempel • 200
0
votes
3
answers
478
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3
answers
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.rempel • 200
0
votes
2
answers
301
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... 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.rempel • 200
2
votes
3
answers
207
views
3
answers
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.rempel • 200
1
vote
3
answers
210
views
3
answers
... 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.rempel • 200
0
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0
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125
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... 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.rempel • 200
0
votes
0
answers
125
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... 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.rempel • 200
Latest awards to e.rempel
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7 days ago,
created a comment with at least 3 up-votes.
For C: Pheatmap error: 'gpar' element 'fill' must not be length 0 , what to do about
Appreciated
12 weeks ago,
created a post with more than 5 votes.
For A: GO analysis using topGO Arabidopsis
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12 weeks ago,
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For A: GO analysis using topGO Arabidopsis
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For A: GO analysis using topGO Arabidopsis
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