User: Ron
Ron • 560
- Reputation:
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Posts by Ron
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... Hi all,
I am doing mutation analysis on RNAseq using rnaseqmut ( https://github.com/davidliwei/rnaseqmut )
.Is there any way to annotate mutations with the actual motifs?
I want to look if some mutations lie in specific motifs of interest e.g. CCAUCG
Thanks,
Ron
...
written 18 days ago by
Ron • 560
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3
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... VirusFinder: Software for Efficient and Accurate Detection of Viruses and Their Integration Sites in Host Genomes through Next Generation Sequencing Data
I came across this software and its easy to install compared to the others,and it gives good results.
e.g. I had some samples positive for viruse ...
written 6 weeks ago by
Ron • 560
0
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1
answer
255
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1
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... Are you still working on getting LM22 signature? ...
written 6 weeks ago by
Ron • 560
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3
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476
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3
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... Were you able to find the older version of Trinity? ...
written 6 weeks ago by
Ron • 560
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1
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198
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... Hi all,
I want to create Silhouette plots in R.
I have the code for that:
library (cluster)
library (vegan)
dis = vegdist(exp_matrix)
res = pam(dis,3) #choice of clustering algorithm
sil = silhouette (res$clustering,dis) # cluster vector
pdf('my_nice_plot.pdf')
plot( ...
written 7 weeks ago by
Ron • 560
• updated
7 weeks ago by
Mattias Aine • 390
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... You can get isoforms expression from Cufflinks in the isoforms.fpkm_tracking file. ...
written 8 weeks ago by
Ron • 560
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3
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205
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Comment:
C: CAGE seq & RNA-seq
... I just want to use FANTOM data which has different cell types and do clustering analysis with regular RNAseq data based on Expression levels.Has anybody done this kind of analysis ?
I am not interested in the primary purpose served by CAGE,thats what I mean.Since FANTOM has multiple cell types Exp ...
written 8 weeks ago by
Ron • 560
0
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2
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159
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2
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Answer:
A: abyss-pe without openmpi
... install ABySS using Linuxbrew. See http://linuxbrew.sh
Install Linuxbrew, and then
brew install homebrew/science/abyss ...
written 8 weeks ago by
Ron • 560
3
votes
3
answers
205
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... Hi all,
I have read this post on CAGEseq and RNA-seq ,and about the differences in their protocols.
https://www.biostars.org/p/155400/
Also,the paper on their comparison which shows they have similar expression profiles:
http://genome.cshlp.org/content/early/2014/03/04/gr.156232.113.long
Howeve ...
written 8 weeks ago by
Ron • 560
• updated
8 weeks ago by
Santosh Anand • 2.2k
0
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... Assuming you have expression data in a matrix of gene vs Samples in the second table
Use melt function from reshape library to get the data in 3 columns format,which will be gene,Sample,Expression Value
library(reshape)
df2_melt= melt(df2,id="gene")
Now you can merge this data with the fir ...
written 10 weeks ago by
Ron • 560
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