Bioconductor CATALYST

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345

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CATALYST

updated 8 weeks ago by SamGG ▴ 300 • written 13 months ago by David • 0

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839

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CATALYST

updated 4 months ago by Hervé Pagès 16k • written 4 months ago by Hyoann ▴ 20

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207

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CATALYST

6 months ago Shaun • 0

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699

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CATALYST

14 months ago David • 0

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805

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CATALYST SingleCellExperiment

updated 2.8 years ago by helucro ▴ 70 • written 2.8 years ago by achaillon • 0

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1.1k

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CATALYST cytofWorkflow

updated 3.8 years ago by Martin Morgan 25k • written 3.8 years ago by Brent.OCarrigan • 0

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759

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CATALYST flowCore assignPrelim Error in vapply read.FCS

4.6 years ago j.krop • 0

7 results • Page 1 of 1

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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…

Votes

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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