User: vignesh

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vignesh90
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Posts by vignesh

<prev • 84 results • page 1 of 9 • next >
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Thankyou Tris. I have an other question. How to check the survival for High and Low expression of a gene? I have gene expression data of TP53 and divided the samples into two groups i.e. High expression and low expression. So, with this I want to see the survival b/w High and low. With your above co ...
written 5 weeks ago by vignesh90
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... Hello, Thanks for putting the code in github. I have seen the just now. But Could you please tell how to use this code for Disease free survival plot? Thank you ...
written 5 weeks ago by vignesh90
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Comment: C: Survival analysis of TCGA patients integrating gene expression (RNASeq) data
... for (i in 1:dim(new_tum)[1]){ if ( sum ( is.na(new_tum[i,])) < dim(new_tum)[2]){ m <- min(new_tum[i,],na.rm=T) new_tum_collapsed <- c(new_tum_collapsed,m) } else { new_tum_collapsed <- c(new_tum_collapsed,'NA') } } You should ope ...
written 5 weeks ago by vignesh90
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Answer: A: [RNAseq] Do anyone have already-built Hisat2 indexes files for human genome (GRC
... Here you can get Indexes for human genome and also other (https://ccb.jhu.edu/software/hisat2/index.shtml) ...
written 6 weeks ago by vignesh90
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Comment: C: How to identify DE lncRNA from RNA Seq Data?
... Hello, could you please tell me which of these annotation files "GRCh37 or GRCh38" has the advantage for identifying lincRNA's? and also why? ...
written 7 weeks ago by vignesh90
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Comment: C: Differential expression analysis for log2(x+1) transformed RSEM normalized count
... This is where I got the data (https://xenabrowser.net/datapages/?dataset=TCGA.LIHC.sampleMap/HiSeqV2&host=https://tcga.xenahubs.net) When I click on the rawdata for download it gives page isn't working. ...
written 9 weeks ago by vignesh90
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Comment: C: Differential expression analysis for log2(x+1) transformed RSEM normalized count
... Thank you. I see that they are using library(curatedCRCData) to get the data. CRC is colorectal. I want the data for liver. I tried giving curatedliverData it says not available. ...
written 9 weeks ago by vignesh90
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Differential expression analysis for log2(x+1) transformed RSEM normalized count (TCGA)
... Hello everyone, I have retrieved the rnaseq data from TCGA. The data is Level_3 Data (file names: *.rsem.genes.normalized_results) downloaded from TCGA, shows the gene-level transcription estimates, as in log2(x+1) transformed RSEM normalized count. Data looks like this: sample TCGA ...
differential analysis R tcga rna-seq written 10 weeks ago by vignesh90 • updated 10 weeks ago by trollchenok0
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... Hi, In the above heatmap how to get all "Basal" subtype as one cluster? I mean all samples showing red should be clustered. In the same way other subtypes also. I see that sample() function which is used for creating fake colors randomly reorders the elements. But I don't want to do that. So how can ...
written 10 weeks ago by vignesh90
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Comment: C: How Do I Draw A Heatmap In R With Both A Color Key And Multiple Color Side Bars?
... Hi, In the above heatmap given by Obi griffith how to get all "Basal" subtype as one cluster? I mean all samples showing red should be clustered. In the same way other subtypes also. I see that sample() function which is used for creating fake colors randomly reorders the elements. But I don't want ...
written 10 weeks ago by vignesh90

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