User: Jon Bråte

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Jon Bråte130
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130
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Location:
Norway
Last seen:
4 weeks, 1 day ago
Joined:
3 years, 12 months ago
Email:
j********@ibv.uio.no

Posts by Jon Bråte

<prev • 56 results • page 1 of 6 • next >
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Comment: C: rtracklayer: how to export gff file with gene names included?
... That solved it, thanks! export(utr, "3_UTR.gff3", format = "GFF3") ...
written 8 months ago by Jon Bråte130
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Answer: A: miRNA-seq data analysis
... This also depends very much on which species you are working on. But check out this recently published online collection of tools. Seems like you can pretty much do the entire pipeline here: http://bioinfo5.ugr.es/srnatoolbox/srnabench/ ...
written 8 months ago by Jon Bråte130
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rtracklayer: how to export gff file with gene names included?
... I'm having trouble understanding the export function in rtracklayer. I have created an object of 3'-UTRs and can export them as gff. But I would like to also include the gene names in the gff-file. They are there in the column Name, but i don't know how to include this in the gff-file. My script: ...
rtracklayer gff written 8 months ago by Jon Bråte130 • updated 8 months ago by Michael Lawrence9.8k
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Comment: C: Why does rlog and vst use normalized counts?
... Thanks for your answer. Now, this might not be an exploratory analysis, but to give a concrete example I have single-cell transcriptome data and I know that all the samples were sequenced to an approximately equal depth. But I have no idea how PCR-bias have influenced the gene expression and what t ...
written 11 months ago by Jon Bråte130
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Why does rlog and vst use normalized counts?
... Hi, For RNAseq data I have used DESeq2's rlog transformed counts for making exploratory plots and quality assessment of my dataset. But I didn't realize that it used normalized counts. I am afraid that this will "force" the samples to look more similar, e.g. in a boxplot of the counts each sample. ...
deseq2 written 11 months ago by Jon Bråte130 • updated 11 months ago by Steve Lianoglou12k
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Answer: A: Test whether expression levels of two gene sets are significantly different
... Hi, Thank you all for valuable and interesting comments. I learned a lot from this. Jon   ...
written 12 months ago by Jon Bråte130
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Comment: C: Test whether expression levels of two gene sets are significantly different
... Thanks! Could I also do a t-test using normalized counts from Deseq? These should take into account differences in sequencing depth, so should be similar to TPMs? The two gene sets are from the same sequencing libraries by the way. ...
written 12 months ago by Jon Bråte130
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Test whether expression levels of two gene sets are significantly different
... Hi, I have a set of non coding genes and a set of coding genes expressed across a number of samples. Based on the boxplots it is obvious that the lncRNAs are expressed lower than coding genes (log2 non-normallized counts). But what is the appropriate test for this kind of data, and is such a test i ...
deseq2 R gene set testing gene expression written 12 months ago by Jon Bråte130
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Answer: A: Error in Knit R Markdown document (could not find function "Biocexptpkg")
... Thanks a lot! Problem solved! :) ...
written 13 months ago by Jon Bråte130
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Error in Knit R Markdown document (could not find function "Biocexptpkg")
... Hi, I am trying to Knit my Rmarkdown file in R Studio, but get this message: Quitting from lines 12-55 (MBV-INFX410-transcriptomics.Rmd) Error in eval(expr, envir, enclos) : could not find function "Biocexptpkg" Calls: <Anonymous> ... in_dir -> inline_exec -> withVisible -> eval ...
rstudio knitr rmarkdown written 13 months ago by Jon Bråte130

Latest awards to Jon Bråte

Great Question 8 months ago, created a question with more than 5,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 8 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 20 months ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 20 months ago, created a question with more than 1,000 views. For Using RNA-Seq raw count data in Weighted Gene Co-Expression Network Analysis
Popular Question 20 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 20 months ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 20 months ago, created a question with more than 1,000 views. For Adjust p-values of a matrix of p-values
Popular Question 2.0 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()

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