Bioconductor Salmon

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3.0k

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tximport dtu salmon TPM rnaseqDTU

written 5.1 years ago by fiona.dick91 ▴ 60

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2.8k

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salmon DESeq2

updated 5 months ago by bella.johnson.2022 • 0 • written 2.3 years ago by Sneha • 0

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1.6k

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salmon edgeR tximport nf-core gene_counts

updated 15 days ago by i.atanasoai • 0 • written 15 months ago by mohammedtoufiq91 ▴ 10

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1.5k

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salmon IsoformSwitchAnalyzeR tximport RNASeqData

updated 9 months ago by k.vitting.seerup ▴ 120 • written 9 months ago by elva.gypsophila ▴ 10

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1.4k

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DESeq2 tximport counts Salmon

updated 10 weeks ago by Michael Love 41k • written 16 months ago by kiqbal • 0

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686

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rna-seq salmon fishpond swish

updated 10 months ago by Michael Love 41k • written 10 months ago by samuelcjx • 0

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428

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salmon tximport deseq2

updated 6 months ago by Michael Love 41k • written 6 months ago by Kayleigh • 0

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305

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swish salmon fishpond

updated 3 months ago by Michael Love 41k • written 3 months ago by Nicholas • 0

8 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19 (as at 4 May 2024). In the meantime, you could consider using the goana() and kegga() …

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

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Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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