Bioconductor GenomicRange

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GenomicRange GenomicRanges

24 months ago • updated 23 months ago mat149 ▴ 80

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DESeq2 version3.16 installation bioconductor GenomicRange

updated 3.1 years ago by James W. MacDonald 68k • written 3.1 years ago by hong • 0

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genomicrange

updated 5.8 years ago by Kevin Blighe ★ 4.0k • written 5.8 years ago by AZ ▴ 20

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genomicrange intersect

updated 5.8 years ago by James W. MacDonald 68k • written 5.8 years ago by AZ ▴ 20

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Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Gordon Smyth 53k

The design matrix that I described above is completely general. I imagine that it would be possible to use the same approach to generate fu…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

Cool, glad to hear I wasn't missing some functionality in DESeq2. I don't know that much about the differences between DESeq2 vs edgeR; my …

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by Michael Love 43k

Yes, so for one thing, note that Gordon has provided code for doing what you are asking in edgeR, which you can go ahead and use. You aske…

Comment: Making a Full Rank Model for Allele-Specific Expression with DESeq2 by chp265 • 0

I don't think DESeq2 has the ability to do multi-contrast comparisons, at least based on what I can understand of the manual; I can pick mu…

Comment: Upcoming Ensembl API and data access changes - new blog post available by Hugo Gruson • 0

Thanks for the update. To be very explicit: what is going to happen to the Biomart service, on which the biomaRt bioconductor package relie…

Votes

A: DESeq2: Is it possible to convert read counts to expression values via TPM and r

A: Filtering read counts matrix: how to deal with duplicated gene symbols, differen

Comment: limpa analysis advice

Answer: When to use edgeR or limma

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