Bioconductor CircRNA

Showing : circRNA • reset

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394

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circRNA circRNAprofiler

2.2 years ago Bogdan ▴ 660

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623

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circRNA RNA-seq circRNAprofiler

3.0 years ago Terra • 0

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883

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DESEQ2 circRNA normalisation

updated 3.8 years ago by Michael Love 40k • written 3.8 years ago by zoe.ward • 0

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686

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deseq2 circRNA rna-editing

updated 3.9 years ago by Michael Love 40k • written 3.9 years ago by maxhenryhills • 0

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923

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deseq2 circrna rsubread

updated 5.3 years ago by Wei Shi ★ 3.5k • written 5.3 years ago by csijst • 0

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1.5k

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deseq2 circrna ciri ciri2

5.4 years ago sbcn ▴ 80

6 results • Page 1 of 1

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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…

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

I get your point as we already starting with TPM. This was more to clarify that I understand the principle correctly. However, further I´m…

Votes

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

Answer: Batch correction and repeated measures

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