User: gokce.ouz

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gokce.ouz40
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New User
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Singapore
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1 year, 1 month ago
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4 years, 7 months ago
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Posts by gokce.ouz

<prev • 34 results • page 1 of 4 • next >
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Comment: C: Mapping Protein Mutation to Genomic DNA
... Thanks for the suggestions Chris Miller. ...
written 15 months ago by gokce.ouz40
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Mapping Protein Mutation to Genomic DNA
... Hi, We have specific protein mutations and we are searching for tools to map these protein mutations to the exact location on the genomic DNA. Do you have any suggestions ? Thanks ...
protein mutation genomic written 15 months ago by gokce.ouz40 • updated 15 months ago by Chris Miller20k
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Comment: C: Filtering Low Count Genes
... Hi h.mon, We are trying to find genes that are significantly differentially expressed to identify as signature genes so we need set of genes that show distinct expressional difference between Mutant vs WT. There is 676 patients in that heatmap: dim(assay(dds) [1] 20502 676 This is ho ...
written 15 months ago by gokce.ouz40
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Comment: C: Filtering Low Count Genes
... Hi Devon, Thanks for your reply. I tried your suggestion, but I have doubts about my method. I made the change at the *results()* function as : res<-results(dds, contrast= c("mutvswt", "Mut", "WT"), filter= rowMedians(counts(dds))) Is this the correct approach ? res[order(res$log2Fold ...
written 15 months ago by gokce.ouz40
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Filtering Low Count Genes
... Hi All, I am working on TCGA Breast Cancer dataset. I downloaded the Count data using **TCGA2STAT.** counts.brca <- getTCGA(disease="BRCA", data.type="RNASeq", type="count") Extracted the mutation data and clinical data using **library("cgdsr")** For downstream analysis I am using **DESe ...
tcga2stat R deseq2 rna-seq written 15 months ago by gokce.ouz40
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... Hi vchris_ngs, I checked the TCGA2STAT. As you said it is what I need,thanks a lot! However, I guess the luck is not on my side, because now, I am getting segfault errors which I posted [here][1] to ask for help. [1]: https://www.biostars.org/p/272544/ ...
written 20 months ago by gokce.ouz40
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segFault error in getTCGA : 'memory not mapped'
... Hi All, I wanted to use TCGA2STAT package to download Breast cancer data. However, I am facing the segfault error. I posted an issue on their github page. But they did not reply back to another user who raised the same issue last January. Therefore, could you please help me solve this problem? Tha ...
tcga2stat R brca rna-seq segfault written 20 months ago by gokce.ouz40
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS release 6.5 (Final) Matrix products: default BLAS: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRblas.so LAPACK: /mnt/software/stow/R-3.4.1/lib64/R/lib/libRlapack.so ...
written 20 months ago by gokce.ouz40
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Comment: C: Alternatives to TCGAbiolinks todownload the TCGA Data
... Thanks a lot for your reply. I will check the alternative you suggested. Also I posted the issue at github, but saw that another user also raised it 8 days ago. Hopefully, they will fix the issue soon. The error occurs when I want to use the library. The installations of R packages are done by syste ...
written 20 months ago by gokce.ouz40
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Comment: C: Error faced for library(TCGAbiolinks)
... Thanks for your reply and clarification. I raised an issue as you suggested. ...
written 20 months ago by gokce.ouz40

Latest awards to gokce.ouz

Popular Question 16 months ago, created a question with more than 1,000 views. For Pre-processing of RNA-Seq data for WGCNA
Popular Question 20 months ago, created a question with more than 1,000 views. For Pre-processing of RNA-Seq data for WGCNA
Popular Question 20 months ago, created a question with more than 1,000 views. For WGCNA- Large number of genes clustering under one Module
Popular Question 20 months ago, created a question with more than 1,000 views. For Pre-processing of RNA-Seq data for WGCNA

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