Bioconductor Spikein

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DiffBind Errorinsocketconnection SpikeIn

9 days ago Virangika • 0

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578

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SpikeIn DiffBind

13 months ago Weisheng • 0

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1.7k

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DESeq2 SpikeIn Normalization DifferentialExpression

updated 14 months ago by ATpoint ★ 4.0k • written 14 months ago by kalavattam ▴ 10

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1.3k

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DESeq2 SpikeIn Normalization

updated 15 months ago by Michael Love 41k • written 15 months ago by kalavattam ▴ 10

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1.6k

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DiffBind SpikeIn Normalization ChIP-seq csaw

16 months ago • updated 15 months ago spg • 0

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898

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DiffBind ChIPSeq Normalization SpikeIn

2.6 years ago Drew • 0

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697

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SpikeIn SingleCell

2.7 years ago mb1996 • 0

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1.1k

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ChIPSeq SpikeIn edgeR Normalization

2.7 years ago maria.soler • 0

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3.7k

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edgeR SpikeIn RNASeq

updated 6 months ago by Miguel • 0 • written 3.2 years ago by robert.chen • 0

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CUTandRUN edgeR Normalization SpikeIn ChIPSeq

updated 17 months ago by Bogdan ▴ 670 • written 3.5 years ago by Hesh ▴ 10

10 results • Page 1 of 1

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Comment: Reproducibility issue with scran together with lapply and BiocParallel by ATpoint ★ 4.0k

Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…

Answer: Reproducibility issue with scran together with lapply and BiocParallel by Aaron Lun ★ 28k

IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…

Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…

Votes

C: null model and DEXSeqDataSet object in DEXSEQ

A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?

A: How to explain how DESeq2 works to someone with zero bioinformatics background?

Answer: Interpret plot from DiffBind

Answer: How to retrieve gene ontology GO class from gene list?

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Supporter to JKim • 0