User: lavanya.kannan
lavanya.kannan • 10
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Posts by lavanya.kannan
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... Thanks for the comments; I made it to work for categorial variables. Now I am trying to add row annotations for categorial variables. In otherwords I am trying to add a heatmap on continuous variables as row annotations for another heatmap. Do I have to to define the bin sizes and treat the continuo ...
written 2.6 years ago by
lavanya.kannan • 10
13
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11 follow
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... I am interested in adding multiple row annotations to my heatmap using the pheatmap function in R (example: https://stackoverflow.com/questions/41628450/r-pheatmap-change-annotation-colors-and-prevent-graphics-window-from-popping-up). The examples I see online all give only one annotation. What is t ...
written 2.7 years ago by
lavanya.kannan • 10
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... ClusterProfiler package: Can I coerce an already generated GSEA results table as a enrichResults object and use it for visualization? ...
written 2.8 years ago by
lavanya.kannan • 10
• updated
6 weeks ago by
emilie.derisoud • 0
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... I am getting the following error while installing the "org.Hs.eg.db" package. I installed vis biocLite and still get the same error. How can I troubleshoot this error?
Thanks,
Lavanya
> install.packages("org.Hs.eg.db", repos="http://bioconductor.org/packages/3.4/data/annotation")
Instal ...
written 2.8 years ago by
lavanya.kannan • 10
• updated
2.8 years ago by
Devon Ryan ♦ 96k
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... Hi,
I am interested in the common motifs in a set of genes that resulted from a DESeq2 analysis. I used the "findMotifs.pl" command of HOMER and got some motifs. Namely, I used
findmotifs.pl genelist.txt mouse $outdir
Now, I am interested in annotating the motifs based on the location in which the ...
written 2.8 years ago by
lavanya.kannan • 10
0
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673
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... Hi,
I am interested in the common motifs in a set of genes that resulted from a DESeq2 analysis. I used the "findMotifs.pl" command of HOMER and got some motifs. Namely, I used
findmotifs.pl genelist.txt mouse $outdir
Now, I am interested in annotating the motifs based on the location in which the ...
written 2.8 years ago by
lavanya.kannan • 10
0
votes
0
answers
525
views
0
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... Hi,
I am interested in the common motifs in a set of genes that resulted from a DESeq2 analysis. I used the "findMotifs.pl" command of HOMER and got some motifs. Namely, I used
findmotifs.pl genelist.txt mouse $outdir
Now, I am interested in annotating the motifs based on the location in which the ...
written 2.8 years ago by
lavanya.kannan • 10
0
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1.9k
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... I am trying to run my preranked rnk file (generated using the DESEQ results). I followed the instructions given in http://genomespot.blogspot.com/2014/09/data-analysis-step-8-pathway-analysis.html to generate it.
When I run the rnk file GSEA, I get the following error:
"After pruning, none of the ...
written 2.9 years ago by
lavanya.kannan • 10
• updated
2.6 years ago by
Biostar ♦♦ 20
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... miso_output/SE/sample1 is the directory where I store all the miso --run results. I tried
summarize_miso ‐‐summarize‐samples miso_output/SE/sample1,
summarize_miso ‐‐summarize‐samples miso_output/SE/
and also
summarize_miso ‐‐summarize‐samples miso_output/
with no luck.
miso_output/SE/ is the di ...
written 3.3 years ago by
lavanya.kannan • 10
0
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758
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... I am trying to run the function "miso_summary" of MISO software (https://miso.readthedocs.io/en/fastmiso/#)
summarize_miso ‐‐summarize‐samples miso_output/SE/sample1 outputdir
but the command does not seem to recognize its arguments - in this case, they are input and output directories. I have ma ...
written 3.3 years ago by
lavanya.kannan • 10
• updated
3.3 years ago by
Pierre Lindenbaum ♦ 129k
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