Bioconductor ColData

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687

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DESeq2 design coldata

updated 6 months ago by swbarnes2 ★ 1.4k • written 6 months ago by arfranco ▴ 130

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811

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ColData pheatmap DESeq2

written 17 months ago by dania.khalid • 0

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1.5k

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SingleCellExperiment colData rename

updated 21 months ago by Basti ▴ 780 • written 21 months ago by achoppe ▴ 10

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714

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BiSeq Coldata

4.5 years ago akhaira • 0

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1.8k

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deseq2 levels factor colData

updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by ariel ▴ 20

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46k

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deseq2 coldata

updated 6.0 years ago by swbarnes2 ★ 1.4k • written 6.0 years ago by mjrarcher ▴ 10

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3.6k

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variantannotation coldata

updated 6.1 years ago by Valerie Obenchain ★ 6.8k • written 6.2 years ago by lvclark ▴ 10

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4.1k

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deseq2 coldata NA

updated 3 months ago by Michael Love 42k • written 6.3 years ago by t.kuilman ▴ 170

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1.7k

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multiassayexperiment colData

updated 7.0 years ago by Levi Waldron ★ 1.1k • written 7.0 years ago by Lluís Revilla Sancho ▴ 760

9 results • Page 1 of 1

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Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 870

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Comment: CleanUpRNAseq with a GTF that is missing mitochondria annotation data by rcreed • 0

The updated version worked well on my data. Thank you!

Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k

The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…

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

Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…

Votes

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

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

A: Error in DESeqDataSet : some values in assay are not integers

A: correcting the batch effects in Limma and SVA

Awards • All

Scholar to Haibo Liu ▴ 20