User: umeshtanwar2

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umeshtanwar210
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Posts by umeshtanwar2

<prev • 34 results • page 1 of 4 • next >
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Comment: C: RNA-Seq Differential gene expression
... Thank you WouterDeCoster. Is there any program/tool to assign the DEGs to the reactome or metabolic pathways in plants? ...
written 7 months ago by umeshtanwar210
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Comment: C: RNA-Seq Differential gene expression
... Thank you arup, but it does not support the plants. ...
written 7 months ago by umeshtanwar210
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RNA-Seq Differential gene expression
... Hi all, I am working on the RNAseq analysis in Arabidopsis plant. I have the list of DEGs which I obtained using DESeq2. I have done the annotation using biomaRt package. Now I would like to assign the DEGs to the Reactome pathways with graphical representation. Could you please help me in this? ...
rna-seq written 7 months ago by umeshtanwar210 • updated 7 months ago by shawn.w.foley1.2k
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Comment: C: Differential gene expression analysis by DESeq2
... Thank you very much Carlo. This is really very helpful. ...
written 10 months ago by umeshtanwar210
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Differential gene expression analysis by DESeq2
... Hi all, I am doing Differential Gene Expression Analysis using DESeq2. I have 8 samples in total (4 treated and 4 untreated) with 3 replicates of each. I am using the the code given below: library(DESeq2) dds <- DESeqDataSetFromMatrix(countData=countdata, colData=coldata, design=~genotyp ...
deseq2 rna-seq lfcthreshold written 10 months ago by umeshtanwar210 • updated 10 months ago by Carlo Yague4.9k
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Comment: C: Running GSEA for DEGs
... I am not using the command line but GSEA Desktop Application. The format of these files looks different from the one you posted. I do not know from which source I can get the gene data sets for Arabidopsis. I could not find Arabidopsis on gsea/msigdb. Could you please suggest some link? Other thing ...
written 11 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you Kevin, It is working now. I have downloaded the gene data sets files for Arabidopsis thaliana from the website [enter link description here][1]. Is this right to use that? It shows error when the GMT formatted file for all gene sets is uploaded. But works well when some of individual dat ...
written 11 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you. I have used this code: rld <- rlogTransformation(dds) head(assay(rld)) hist(assay(rld)) write.table(assay(rld), file="gsea.txt") I obtained this file: > "A_m1" "A_m2" "A_m3" "A_t1" "A_t2" "A_t3" "B_m1" "B_m2" "B_m3" "B_t1" "B_t2" "B_t3" "C_m1" "C_m2" "C_m3" "C ...
written 11 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Yes, its Arabidopsis. ...
written 11 months ago by umeshtanwar210
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Comment: C: Running GSEA for DEGs
... Thank you @Kevin. I am new for this kind of analysis. In total I have 8 samples (4 treated and 4 untreated) with 3 replicates. countdata <- read.table("NewTotalCounts.txt", header=TRUE, row.names=1) countdata <- countdata[ ,6:ncol(countdata)] countdata <- as.matrix(countdata) ...
written 11 months ago by umeshtanwar210

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