User: manali.rupji

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manali.rupji10
Reputation:
10
Status:
New User
Location:
United States
Last seen:
1 month, 1 week ago
Joined:
4 years, 9 months ago
Email:
m***********@emory.edu

Posts by manali.rupji

<prev • 24 results • page 1 of 3 • next >
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TCGA normal vs control sample
... Hello All, In the TCGA database, based on the barcode, 01-9 are tumors, 11-19 are normals and control samples are labeled 20 - 29. I am unable to find in the TCGA documentation what is the difference between the controls and normals? I understand normals are surrounding tissues that are used from ...
tcga rna-seq written 6 weeks ago by manali.rupji10
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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 2.3 years ago by manali.rupji10
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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 2.3 years ago by manali.rupji10
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Comment: C: Create workflows for behind the scene processes
... Yes and within a shiny application. ...
written 2.3 years ago by manali.rupji10
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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 2.3 years ago by manali.rupji10
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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 2.3 years ago by manali.rupji10 • updated 2.3 years ago by genomax83k
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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 2.4 years ago by manali.rupji10
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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 2.5 years ago by manali.rupji10
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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 2.5 years ago by manali.rupji10
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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 2.5 years ago by manali.rupji10

Latest awards to manali.rupji

Popular Question 2.2 years ago, created a question with more than 1,000 views. For List of house keeping genes for hg19
Popular Question 2.2 years ago, created a question with more than 1,000 views. For shiny app example hosted on aws
Popular Question 2.2 years ago, created a question with more than 1,000 views. For GSEA with variant proportions as input
Popular Question 2.2 years ago, created a question with more than 1,000 views. For How to extract plots from ConsensusClusterPlus package
Popular Question 2.2 years ago, created a question with more than 1,000 views. For Gold standard cell lines with characteristic gene fusions for Breast Cancer

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