User: da.de

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da.de10
Reputation:
10
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New User
Location:
Austria
Last seen:
3 months, 1 week ago
Joined:
3 years, 3 months ago
Email:
d****@gmx.net

Posts by da.de

<prev • 10 results • page 1 of 1 • next >
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Comment: C: Add annotation color bar to ggplot
... I have a bar plot with 150 samples of different groups. Some of them are negative. If I color the bars I do not see the difference between the groups, that's why I wanted to add the annotation like it is used in pheatmap. Just to show that all groups are represented equally ...
written 3 months ago by da.de10
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Add annotation color bar to ggplot
... Hi, I want to add annotation color to a normal ggplots2 figure (barplot) like it is used for example in pheatmap. pheatmap(assay(ntd)[select,], cluster_rows=FALSE, show_rownames=FALSE, cluster_cols=FALSE, annotation_col=df) For a pheatmap I add a df for annoation_col. How can I do it for other fi ...
annotation ggplot2 written 4 months ago by da.de10 • updated 4 months ago by TriS200
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Job: Senior Bioinformatician, Children's Cancer Research Institute Vienna, Austria
... Senior Bioinformatician, Children´s Cancer Research Institute Vienna The Children´s Cancer Research Institute (science.ccri.at) announces recruitment for the position of a senior bioinformatician. The St. Anna Kinderspital (StA) and the Children´s Cancer Research Institute (CCRI) are known for prov ...
rnaseq job ngs bioinformatician job postdoc wgs written 6 months ago by da.de10
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DESeq2: same count matrix, different design
... Dear all, I am a beginner and have the following problem. I have a dds object and run DESeq two times using exactly the same count matrix but different design. (1)  why is the baseMean of dds1 not the same as the baseMean of dds2? I thought the baseMean is only normalized by sizeFactor. (2) I also ...
deseq2 basemean cooks distance written 6 months ago by da.de10 • updated 6 months ago by Michael Love19k
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Extract info from smc object
... Dear all, I have a very basic question: I have a list of smc objects and I want to extract the info available in slot "ids". How can I do that? The list was creted using the readGmt function from the PGSEA package. However, I do not have the original gmt file. Below you find an example of one of t ...
pgsea smc object written 7 months ago by da.de10
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DESeq2 model with blocking factor + interaction term
... Hi, I am using DESeq2 for the analysis of my RNAseq data. I have the following sample set up: Condition         Treatment Luc2                   no Luc2                   DOX ProtA                 no ProtA                 DOX ProtB                 no ProtB                 DOX A cell line inducib ...
deseq2 model written 3.1 years ago by da.de10 • updated 3.1 years ago by Simon Anders3.5k
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How to add search functions and additional fields to the html file of DESeq2 results created with ReportingTools
... Hi, I started using the ReportingTools Package to visualize DESeq2 results including a ggplot2 graph, links and metadata. I really like the resulting html report. However, I am looking for a way how to add some features: Automatically there is a filter option for numeric columns in the html rep ...
reportingtools deseq2 hwriter written 3.1 years ago by da.de10 • updated 3.1 years ago by James W. MacDonald47k
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Comment: C: ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
... Hi, thanks for your reply. I found out why it did not keep the names. I only had them as a metadata column gr1$names not as names(gr1). I changed this and now it works. However, any suggestions how to keep the metadata? ...
written 3.3 years ago by da.de10
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ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata
... Hi, I am using the findOverlapsOfPeaks function from the ChIPpeakAnno_3.2.0 package. Is there a possibility to keep the metadata of the GRanges objects used for the overlap? Would be nice to have it in the output (peaklist GRanges). Or to at least keep the peak names from the input. For me it see ...
chippeakanno findoverlapsofpeaks written 3.3 years ago by da.de10 • updated 3.2 years ago by Hari Easwaran240
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Scaled venn/euler diagram using makeVennDiagram
... Hi, I am using the ChIPpeakAnno package for analysis of my ChIPseq data. However, I am having some problems with the makeVennDiagramm function. I have three datasets to overlap. And although I am using the euler and scaled=TRUE I do not succeed in getting a scaled diagram. makeVennDiagram (RangedD ...
chippeakanno venn diagram written 3.3 years ago by da.de10 • updated 3.3 years ago by Ou, Jianhong1.1k

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Popular Question 2.7 years ago, created a question with more than 1,000 views. For ChIPpeakAnno: findOverlapsOfPeaks keep GRanges metadata

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