User: Kasthuri

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Kasthuri260
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9 years, 6 months ago
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Posts by Kasthuri

<prev • 64 results • page 1 of 7 • next >
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Driver analysis MutPanning trouble
... Has anyone tried MutPanning, a driver-passenger analysis? http://www.cancer-genes.org/ I tried using it locally as well as on GenePattern, but I get this error: Launching MutPanning with root file /mutpanning_temp Aligning Maf to Hg19 0 123 1 117 java.lang.NullPointerException ...
driver-passenger analysis next-gen written 19 days ago by Kasthuri260 • updated 7 days ago by android890
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Comment: C: Enhancer prediction for Glioma Stem Cells (ChIP-Seq)
... No, not histones. TFs - knock out of a gene - ...
written 7 months 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 7 months 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 7 months ago by Kasthuri260
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Comment: C: EdgeR differential expression and heatmap
... Thanks, I figured out. ...
written 14 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 14 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 14 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 14 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 14 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 14 months ago by Kasthuri260

Latest awards to Kasthuri

Appreciated 7 months ago, created a post with more than 5 votes. For Whole Exome From Whole Genome
Popular Question 7 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Popular Question 7 months ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Popular Question 7 months ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Scholar 7 months ago, created an answer that has been accepted. For A: deepTools white dots on black background
Popular Question 12 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Popular Question 13 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Popular Question 19 months ago, created a question with more than 1,000 views. For KeyError in MACS2
Popular Question 19 months ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Student 19 months ago, asked a question with at least 3 up-votes. For Tools For Structural Variants
Epic Question 2.7 years ago, created a question with more than 10,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 2.7 years ago, created a question with more than 1,000 views. For KeyError in MACS2
Popular Question 2.8 years ago, created a question with more than 1,000 views. For Identifying germline and tumor samples
Appreciated 2.9 years ago, created a post with more than 5 votes. For How To Visually Display What Protein Domains Are Affected By A Mutation
Great Question 2.9 years ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Student 4.0 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome
Popular Question 4.0 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Whole Exome From Whole Genome
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Chip-Seq Txt Data Into Sam Format.
Great Question 5.5 years ago, created a question with more than 5,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 5.5 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Popular Question 5.8 years ago, created a question with more than 1,000 views. For Vcf To Maf (Mutation Annotation Format) Conversion ?
Student 7.1 years ago, asked a question with at least 3 up-votes. For How To Visually Display What Protein Domains Are Affected By A Mutation
Student 8.2 years ago, asked a question with at least 3 up-votes. For Whole Exome From Whole Genome

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