User: manali.rupji

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Posts by manali.rupji

<prev • 17 results • page 1 of 2 • next >
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Parallelize consensusClusterPlus package
... Hi All, I am using consensus cluster package as a part of a shiny tool for genomic data. This package runs on my local machine in about a minute but takes almost 15-20 mins to run on the virtual machine instance. What are the possible solutions to increase the computational speed of the package? I ...
consensusclusterplus parallelize written 1 day ago by manali.rupji0
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How to extract plots from ConsensusClusterPlus package
... Hello All, Is there a way to extract the plots separately from the ConsensusClusterPlus package? For example, using the example data from the package, I can print the last three plots as below, library(ALL) data(ALL) d=exprs(ALL) mads=apply(d,1,mad) d=d[rev(order(mads))[1: ...
consensusclusterplus plots written 4 days ago by manali.rupji0
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Answer: A: Need Cluster of cluster analysis steps
... Hi Mamta, CoC analysis is basically based on the cluster information from various platforms(miRNA, mRNA, methylation, CNV, etc). The basic Idea being, you should have the same number of samples in each platform and some way of clustering them. It can be NMF, heatmap clustering, kmeans, etc. So say ...
written 4 days ago by manali.rupji0
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Comment: C: shiny app example hosted on aws
... Yes, indeed. Nothing else is running on the server which is concerning here. ...
written 7 days ago by manali.rupji0
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Comment: C: shiny app example hosted on aws
... Thanks Sean. Surely. Any idea how much that would cost ? As that could be a huge limitation for us. I have tried using code to test what could be causing the app to slow down as well but that is typically due to a specific R package that is running. I am also looking into other packages which could ...
written 13 days ago by manali.rupji0
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Comment: C: shiny app example hosted on aws
... Thank you for the information. ...
written 13 days ago by manali.rupji0
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Comment: C: shiny app example hosted on aws
... Thank you Devon. Yes, it is a Virtual server and i'm afraid it is set up to do one web process per application. Thus, when one person is accessing it, the second user can hardly get it to even load. ...
written 13 days ago by manali.rupji0
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Comment: C: shiny app example hosted on aws
... Thank you for your insightful comments. The process runs on my local computer (32 GB RAM, core i-7, 2.90 GHZ, 4 core, 8 processors) in about 2 mins but the same takes about 20 mins when hosted as a web-link on the Centos server (14 GB total memory, x86_64, 1 thread per core, 2 cores per socket, 2 so ...
written 14 days ago by manali.rupji0
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shiny app example hosted on aws
... Hello All, Could someone guide me towards an example computationally intensive shiny app hosted on the Amazon Web Server? I am unable to find a good example. I would like to show this example to gain support from the IT department to move to use AWS for my recently created shiny app which runs ext ...
aws shiny app written 14 days ago by manali.rupji0
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List of house keeping genes for hg19
... Hello all, Could someone please direct me to a database containing all human genome 19, house keeping gene list? Thanks in advance. ...
house keeping genes hg19 written 7 months ago by manali.rupji0 • updated 7 months ago by Santosh Anand3.0k

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