Bioconductor Variantfiltering

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bioconductor variantfiltering

6.7 years ago Claus.Hultschig • 0

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variantannotation variantfiltering

updated 7.1 years ago by Michael Lawrence ★ 11k • written 7.1 years ago by Bogdan ▴ 670

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346

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VariantFiltering

updated 10 months ago by Robert Castelo ★ 3.3k • written 10 months ago by Andrew Beggs ▴ 90

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VariantFiltering

8.8 years ago claire.simpson • 0

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RNAseq123 VariantFiltering Alignment VariantAnnotation

updated 17 months ago by James W. MacDonald 65k • written 17 months ago by Mohamed ▴ 30

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variantfiltering phastcons

updated 9.0 years ago by Robert Castelo ★ 3.3k • written 9.0 years ago by Stefanie Tauber ▴ 40

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439

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VariantAnnotation VariantFiltering

7 months ago Bogdan ▴ 670

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sequencing transcription variantfiltering annotation News

8.9 years ago Matthew Ritchie ▴ 1000

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VariantFiltering VariantFiltering

9.9 years ago Robert Castelo ★ 3.3k

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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