Bioconductor Scater

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365

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scater runPCA

updated 4 weeks ago by alan.ocallaghan ▴ 160 • written 4 weeks ago by Najla Abassi • 0

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221

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scran bluster scater scuttle

updated 4 weeks ago by ATpoint ★ 4.0k • written 4 weeks ago by Dario Strbenac ★ 1.5k

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333

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scater

updated 12 weeks ago by alan.ocallaghan ▴ 160 • written 12 weeks ago by Dario Strbenac ★ 1.5k

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231

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scater

updated 12 weeks ago by alan.ocallaghan ▴ 160 • written 12 weeks ago by Dario Strbenac ★ 1.5k

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6.4k

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runUMAP scater Matrix

updated 7 weeks ago by Hervé Pagès 16k • written 5 months ago by inzirio ▴ 10

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1.1k

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scuttle scater

updated 7 months ago by ATpoint ★ 4.0k • written 7 months ago by Abbi Edwards • 0

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856

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plotHeatmap scater

10 months ago Alina • 0

7 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