Bioconductor Bsgenomeforge

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BSgenomeForge

15 days ago Bruno • 0

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379

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BSgenomeForge BSgenome

updated 3 months ago by James W. MacDonald 63k • written 3 months ago by kyliecode • 0

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1.4k

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BSGenomeForge BSGenome

updated 2.5 years ago by Hervé Pagès 16k • written 2.5 years ago by sieminsk • 0

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1.2k

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cleanUpdTSeq BSgenome BSgenomeForge

updated 4.6 years ago by Julie Zhu ★ 4.3k • written 4.6 years ago by danielle.bilodeau • 0

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933

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BSgenomeForge

7.0 years ago • updated 6.9 years ago Vijay Lakhujani • 0

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Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

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Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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