User: Jon Bråte

gravatar for Jon Bråte
Jon Bråte150
Reputation:
150
Status:
Trusted
Location:
Norway
Last seen:
3 weeks, 4 days ago
Joined:
5 years, 4 months ago
Email:
j********@ibv.uio.no

Posts by Jon Bråte

<prev • 62 results • page 1 of 7 • next >
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Comment: C: How to remove samples from EDAseq SeqExpressionSeq
... Thanks! That's perfect. Jon ...
written 3 months ago by Jon Bråte150
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How to remove samples from EDAseq SeqExpressionSeq
... I have created a new `SeqExpressionSet` and I would like to remove different samples to see the effects on downstream analyses. Can I remove the samples, including the metadata information, directly from the `SeqExpressionSet`? Here is my object: > set SeqExpressionSet (storageMode: loc ...
edaseq written 3 months ago by Jon Bråte150 • updated 3 months ago by davide risso810
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Comment: C: DESeq2: How to get sizeFactor per library when importing counts with tximport?
... Perfect! Thanks!! ...
written 12 months ago by Jon Bråte150
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DESeq2: How to get sizeFactor per library when importing counts with tximport?
... This is the first time I've tried to import Kallisto output using tximport for use in DESeq2. I want to get the sizeFactors calculated by DEseq2 and use them for normalizating counts from another experiment. But I am only able to get size factors for each gene individually (normalizationFactors(dds) ...
deseq2 written 12 months ago by Jon Bråte150 • updated 12 months ago by Michael Love23k
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Comment: C: DESeq2: Question about the alpha in summary() and results()
... I see, thanks! ...
written 15 months ago by Jon Bråte150
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DESeq2: Question about the alpha in summary() and results()
... I'm getting slight differences when setting the alpha to 0.05 with the results() function and the summary() function. Is this correct, or am I doing something wrong? Thanks, Jon   > res <- results(dds) > summary(res) out of 29391 with nonzero total read count adjusted p-value < 0.1 ...
deseq2 written 15 months ago by Jon Bråte150 • updated 15 months ago by Michael Love23k
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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 2.1 years ago by Jon Bråte150
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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 2.1 years ago by Jon Bråte150
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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 2.1 years ago by Jon Bråte150 • updated 2.1 years ago by Michael Lawrence10k
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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 2.3 years ago by Jon Bråte150

Latest awards to Jon Bråte

Epic Question 9 months ago, created a question with more than 10,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 9 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 12 months ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Supporter 2.1 years ago, voted at least 25 times.
Great Question 2.1 years ago, created a question with more than 5,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Use R/Bioconductor to match BLAST hits to GO terms?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 2.1 years ago, created a question with more than 1,000 views. For (how) can I make heatmaps/PCA in DESeq2 using normalized counts from cummeRbund?
Popular Question 2.1 years 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 2.1 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 2.1 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Differential expression of RNA-seq data using limma and voom()
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Rearrange dendrogram to match merged modules in WGCNA?
Popular Question 3.1 years ago, created a question with more than 1,000 views. For Adjust p-values of a matrix of p-values
Popular Question 3.1 years 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 3.1 years ago, created a question with more than 1,000 views. For Error running TOMplot in WGCNA package
Popular Question 3.4 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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