Bioconductor Salmon

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tximport dtu salmon TPM rnaseqDTU

written 5.1 years ago by fiona.dick91 ▴ 60

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salmon edgeR tximport nf-core gene_counts

updated 12 days ago by i.atanasoai • 0 • written 14 months ago by mohammedtoufiq91 ▴ 10

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DESeq2 tximport counts Salmon

updated 9 weeks ago by Michael Love 41k • written 16 months ago by kiqbal • 0

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424

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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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677

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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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301

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swish salmon fishpond

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

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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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salmon DESeq2

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

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Comment: Store output of matchPWM() by James W. MacDonald 65k

Here's a self contained reproducible example, using part of the example in `?matchPWM` ``` > library(Biostrings) > data(HNF4alpha) > libr…

Comment: DEseq2 coefficient by JKim • 0

Hi Dr. Love, I'm sorry to ask another question to my old post. If the design isn't balanced, the interpretation of coefficients will be…

Comment: Store output of matchPWM() by mat149 ▴ 70

out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) Error in do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) : '…

Answer: Store output of matchPWM() by James W. MacDonald 65k

Something like this? ``` ind <- as.logical(sapply(hitlist, length)) out <- do.call(c, lapply(hitlist, function(x) as(x, "IRanges"))) …

Answer: log2FoldChange value is way too different when compared with counts(dds) by Michael Love 41k

This has been asked before, but with a multi factor design, the LFC for coefficient X adjust for the others, in a way that is often hard to…

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SPIA plotP giving error

Answer: Fold change calculation in Diffbind vs. DESEQ2?

C: How to establish a subset from TxDb.Hsapiens.UCSC.hg38.knownGene DB

C: Extremely big genes in annotation TxDb packages

Make custom Txdb class objects from Txdb

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