Bioconductor Salmon

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289

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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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408

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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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1.4k

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salmon IsoformSwitchAnalyzeR tximport RNASeqData

updated 8 months ago by k.vitting.seerup ▴ 120 • written 9 months ago by elva.gypsophila ▴ 10

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666

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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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1.5k

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salmon edgeR tximport nf-core gene_counts

updated 5 days ago by i.atanasoai • 0 • written 14 months ago by mohammedtoufiq91 ▴ 10

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1.3k

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DESeq2 tximport counts Salmon

updated 8 weeks ago by Michael Love 41k • written 16 months ago by kiqbal • 0

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2.8k

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salmon DESeq2

updated 4 months ago by bella.johnson.2022 • 0 • written 2.3 years ago by Sneha • 0

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2.9k

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tximport dtu salmon TPM rnaseqDTU

written 5.1 years ago by fiona.dick91 ▴ 60

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Comment: Error for AnnotationForge makeOrgPackageFromNCBI function by James W. MacDonald 65k

That's weird. I don't have any problem at all generating the `OrgDb` on my box. How big is the gene2pubmed.gz file? I get this: ``` gzip -…

Answer: get BM error by James W. MacDonald 65k

The genes you present are orthologous mappings from D. rerio to other teleost fishes, so it is probably going to be difficult to map to NCB…

Answer: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k

You can also use a combination of the `org.Hs.eg.db` and `GO.db` packages. ``` > library(GO.db) > library(org.Hs.eg.db) > go <- m…

Comment: Different Shrunk Log2FC according with reference by Michael Love 41k

I took a look and the posterior width for these (fairly rare) examples overlaps zero. So the posterior when it disagrees is not narrow. An…

Comment: How to tell and visualize up/down regulation of pathways from clusterprofiler gs by Guangchuang Yu ★ 1.2k

an example is also presented in <https://pubmed.ncbi.nlm.nih.gov/34557778/>.

Votes

Reproducibility issue with scran together with lapply and BiocParallel

C: SGSeq: moving toward diffex from SGSeq analysis

DEXSeq-Error in FUN(X[[i]], ...) : subscript out of bounds

Subset DEXSeqDataSet In DEXSeq

How to get all possible comparisons in DiffBind

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