User: Björn

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Björn20
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Posts by Björn

<prev • 58 results • page 1 of 6 • next >
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How to find miRNAs of interest in TCGA ?
... How to find if for e.g. let-7a is associated with any cancer in TCGA database. Is there any specific ways to present such data in standard format. ...
tcga rna-seq written 9 days ago by Björn20
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How to present up and down regulated, and unchanged miRNAs in paired samples using Rstudio?
... Is there a way to present up and down regulated, and unchanged miRNAs in paired samples using Rstudio (e.g. venn diagram or bar chart)? Does "contrasts" used in edgeR applicable to list such miRNA expression. ...
R venn diagram rna-seq mirna written 9 days ago by Björn20 • updated 1 day ago by Biostar ♦♦ 20
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Comment: C: MicroRNA-target interactions databases
... Hi, I am interested in the first one. Thanks ...
written 10 days ago by Björn20
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Comment: A: MicroRNA-target interactions databases
... @kevin Blighe Nice thread..how to create the two graphs that you showed here. For example, I have two miRNAs: hsa-let-7a, and hsa-miR-4511 ...
written 11 days ago by Björn20
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what is the function of prior.count in lcpm ?
... In this command line while using edgeR, `lcpm<-cpm(y,prior.count=5, log=T)` what is the applicability of `prior.count` there ? I found "prior.count as average count to be added to each observation to avoid taking log of zero. Used only if log=TRUE." Is there any range to be used ? How to know w ...
lcpm rna-seq edger written 12 days ago by Björn20
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How to create heatmaps only with DE genes in edgeR
... Now I have 20 DE genes out of 500 genes between groups A and B. How can I create heatmaps only with those 20 DE genes? See figure S1 and S3 from the [reference paper][1][1]: http://www.pnas.org/content/113/38/10655 I created figure S1 using `heatmap.2` in Rstudio- edgeR. ...
pheatmap heatmap.2 de genes edger written 19 days ago by Björn20 • updated 19 days ago by Wietje120
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Why DE genes are not among highly variable genes between groups
... I got list of "highly variable genes" between Groups A x B using variance in edgeR (ref: [highly variable genes][1]) Then performed standard edgeR analysis to find DE genes. [ref: edgeR][2] PROBLEM: Why none of the DE genes between A x B are included in "highly variable genes" My questions 1. Wha ...
variance edger mirna written 23 days ago by Björn20 • updated 23 days ago by Devon Ryan79k
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I have few Differentially expressed miRNAs out of edgeR ?
... I have found Differentially expressed miRNAs out of edgeR. What are next steps for pathway analysis ? Any literature would be appreciated. I used Targetscan to find genes that are associated with individual miRNAs. But I believe there are many other steps to perform before I can finally prepare resu ...
enrichment analysis pathway analysis go mirnas written 27 days ago by Björn20
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Comment: C: How to reorder column vectors in r to use for heatmap.2
... It reorders the vectors but not in the heatmap. ...
written 4 weeks ago by Björn20
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How to reorder column vectors in r to use for heatmap.2
... I have a column (country) with vectors in a file xyz which is a data.frame Country Germany Switzerland Germany Germany Switzerland How can I reorder it to same countries. Germany Germany Germany Switzerland Switzerland The reordering must generate t ...
vector column heatmap.2 written 4 weeks ago by Björn20

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