Bioconductor Ncrna

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computational biology molecular biology RNA r-loop ncRNA Job

6.5 years ago l.brown ▴ 10

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grch37 transcripts biotype biomaRt ncrna

updated 6.7 years ago by James W. MacDonald 68k • written 6.7 years ago by sergio.martinezcuesta ▴ 10

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gsea ncrna coexpression gene set analysis gene set testing

9.0 years ago m.fletcher ▴ 20

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biomart ncrna

updated 9.6 years ago by Thomas Maurel ▴ 800 • written 9.6 years ago by Zhang,Jiexin ▴ 20

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trna ncrna genomicfeatures featuredb biomart

updated 10.0 years ago by Hervé Pagès 16k • written 10.1 years ago by Keith Hughitt ▴ 180

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Comment: Differing results with DESeq2 by JKim • 0

My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …

Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k

Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…

Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k

This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…

Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80

Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…

Answer: Analyzing TnSeq data with DESeq2 by cold.wolverine.arku • 0

That's a great use case of DESeq2! Even though it's not specifically tailored for TnSeq data, your approach to normalize and run explorator…

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A: Understanding contrasts limma

Answer: ROAST for small sets

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