User: lavanya.kannan

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Posts by lavanya.kannan

<prev • 13 results • page 1 of 2 • next >
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Comment: A: how to display multiple row annotations on pheatmap
... 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 23 months ago by lavanya.kannan0
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how to display multiple row annotations on pheatmap
... 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 ...
pheatmap written 2.0 years ago by lavanya.kannan0
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Pathways visualization for GSEA table input in ClusterProfiler package of Bioconductor
... ClusterProfiler package: Can I coerce an already generated GSEA results table as a enrichResults object and use it for visualization? ...
bioconductor clusterprofiler written 2.1 years ago by lavanya.kannan0 • updated 2.1 years ago by Guangchuang Yu2.3k
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error installing "org.Hs.eg.db"
... 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 ...
bioconductor written 2.1 years ago by lavanya.kannan0 • updated 2.1 years ago by Devon Ryan93k
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how do I use Homer with custom regions?
... 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 ...
homer written 2.1 years ago by lavanya.kannan0
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finding rna motifs in the 3' or 5' regions using RNASeq using DESeq2 genesets
... 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 ...
rna-seq written 2.1 years ago by lavanya.kannan0
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(Closed) finding rna motifs in the 3' or 5' regions using RNASeq using DESeq2 genesets
... 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 ...
rna-seq written 2.1 years ago by lavanya.kannan0
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running DESEQ2 results in GSEA
... 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 ...
rna-seq written 2.2 years ago by lavanya.kannan0 • updated 23 months ago by Biostar ♦♦ 20
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Comment: C: summarize_miso not recognizing my directories
... 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 2.6 years ago by lavanya.kannan0
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summarize_miso not recognizing my directories
... 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 ...
rna-seq written 2.6 years ago by lavanya.kannan0 • updated 2.6 years ago by Pierre Lindenbaum124k

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