Bioconductor Spike-in

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 15 months ago by manuel.fernandez • 0 • written 2.6 years ago by cicely.day • 0

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deseq2 apeglm rna-seq spike-in

updated 4.3 years ago by Michael Love 42k • written 4.3 years ago by nadezda.fursova ▴ 10

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2.5k

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deseq2 Tximport Sizefactors normalizationfactors spike-in

updated 4.4 years ago by Michael Love 42k • written 4.4 years ago by Hina Bandukwala • 0

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1.3k

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scran spike-in

6.7 years ago • updated 6.6 years ago supremerulersuraj • 0

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3.6k

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deseq2 ruvseq spike-in time course time series

updated 7.0 years ago by davide risso ▴ 980 • written 7.0 years ago by staceyborrego ▴ 20

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Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by Paul • 0

You are an absolute lifesaver, thank you so much for the clarification!

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

The `EnsDb.Mmusculus.v79` package is mm38, not mm39. If you want a current `EnsDb`, use `AnnotationHub` ``` > library(AnnotationHub) >…

Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

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Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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