User: Kasthuri

gravatar for Kasthuri
Kasthuri260
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260
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1 month ago
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8 years, 11 months ago
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k*******@gmail.com

Posts by Kasthuri

<prev • 63 results • page 1 of 7 • next >
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Comment: C: Enhancer prediction for Glioma Stem Cells (ChIP-Seq)
... No, not histones. TFs - knock out of a gene - ...
written 4 weeks ago by Kasthuri260
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Comment: C: Enhancer prediction for Glioma Stem Cells (ChIP-Seq)
... Do you mean like the file format? - It is bed format. It's from human-derived glioma stem cells (GSCs) - both control and experiment. Is this what you are asking? ...
written 4 weeks ago by Kasthuri260
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Enhancer prediction for Glioma Stem Cells (ChIP-Seq)
... I am trying to predict enhancer regions in the ChIP-Seq data derived from Glioma Stem Cells (human). I already have aligned the data to hg19 and called the peaks. I understand ChromHMM and Encode annotations for histone marks may do the trick but I am lost on the step by step procedure since this ce ...
enhancer chip-seq written 5 weeks ago by Kasthuri260
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Comment: C: EdgeR differential expression and heatmap
... Thanks, I figured out. ...
written 7 months ago by Kasthuri260
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EdgeR differential expression and heatmap
... I performed a differential gene expression analysis for the red vs. blue group as shown in this image below (RNA-seq data) using TCGAbiolinks which uses the EdgeR package. Clearly, there is a difference between the groups however the difference is due to under-expression in **some** samples in the b ...
rna-seq written 7 months ago by Kasthuri260
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Comment: C: Error in GDCprepare
... Yes, it works for me and I processed my data. Hopefully, they shouldn't change the code at TCGAbiolinks. ...
written 7 months ago by Kasthuri260
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Comment: C: Error in GDCprepare
... Ok, I figured out. If we are using the new query as suggested, we need to use `geneInfo = geneInfoHT` option in the `TCGAanalyze_Normalization` function. Thus, it should be, Norm.Mat.C1 <- TCGAanalyze_Normalization(tabDF = Matrix.C1, geneInfo = geneInfoHT) However, using this updated prot ...
written 7 months ago by Kasthuri260
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Comment: C: Error in GDCprepare
... Thanks a lot, noorpratap.singh. However, I get errors down the line, now. listSamples <- Cluster.1.df$`Sample ID` library(SummarizedExperiment) query <- GDCquery(project = "TCGA-BRCA", data.category = "Transcriptome Profiling", data.t ...
written 7 months ago by Kasthuri260
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Comment: C: Error in GDCprepare
... Thanks! I updated it and still have problems. Here is the full query - it is exactly as posted in their [manual][1] library(TCGAbiolinks) library(SummarizedExperiment) # You can define a list of samples to query and download providing relative TCGA barcodes. listSamples &l ...
written 7 months ago by Kasthuri260
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Error in GDCprepare
... I am working with RNA seq data from TCGA using TCGAbiolinks. Everything has been working fine so far and suddenly I get this error: > RnaseqSE <- GDCprepare(query) |=================================================================================| 100% Error in fix.by(by.y, y) : ' ...
tcga written 7 months ago by Kasthuri260

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