User: manali.rupji

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Posts by manali.rupji

<prev • 23 results • page 1 of 3 • next >
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Comment: C: Create workflows for behind the scene processes
... Playing within R would be handy so we could customize based on the number of steps the user decides to perform. Thanks for your input. ...
written 6 months ago by manali.rupji0
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Comment: C: Create workflows for behind the scene processes
... Thanks! Yes, I came across that package, thanks for your advice. I 'll try using that. ...
written 6 months ago by manali.rupji0
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Comment: C: Create workflows for behind the scene processes
... Yes and within a shiny application. ...
written 6 months ago by manali.rupji0
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Create workflows for behind the scene processes
... Hello All, I wish to incorporate a workflow image (like Galaxy workflow) for my multi-step R/shiny application. Basically, I wish to provide the user with the exact input or parameters that were used at each step in forms of a flowchart output. What could be a potential solution to achieve this? ...
R shiny tensorflow written 6 months ago by manali.rupji0
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Matched pair analysis for small sample size
... Hello All, I have a data set for analysis provided to me. It includes 3 matched paired samples i.e. Diagnostic vs Recurrent. Also provided to me are a set of genes (group A = 30 genes) and a set of genes (not A = 2000 genes) based on some previous analysis on another sample set. I was told that the ...
matched rna small sample size written 6 months ago by manali.rupji0 • updated 6 months ago by genomax54k
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Can PAM50 classification performed on TCGA-BRCA RNASeq RSEM data be used with RNASeq FPKM normalized data for downstream analysis?
... Hi Everyone, I was provided with TCGA-BRCA RNASeq V2 FPKM Tumor-Normal matched data which I intended to perform downstream analysis on. I also have the PAM50 classification based on an older downloaded TCGA-BRCA RNASeq V2 RSEM normalization for the same tumor-normal matched pairs. Is it correct t ...
normalization pam50 rna-seq written 7 months ago by manali.rupji0
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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 8 months 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 8 months 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 8 months 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 8 months ago by manali.rupji0

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