Bioconductor Workflow

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Bioconductor Workflow

updated 2.3 years ago by Gordon Smyth 50k • written 2.3 years ago by sarastew1994 • 0

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Workflow Software ExperimentData Deprecation

3.4 years ago • updated 3.0 years ago shepherl 3.8k

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RNA-Seq Workflow

updated 4.9 years ago by Gordon Smyth 50k • written 4.9 years ago by detroit.drive • 0

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756

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rnaseqGene workflow deseq2

updated 4.3 years ago by Michael Love 41k • written 4.3 years ago by Assa Yeroslaviz ★ 1.5k

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780

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Software annotation experiment workflow

updated 3.7 years ago by shepherl 3.8k • written 3.7 years ago by gnanaprakash.s • 0

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software error deseq2 workflow rnaseqGene

updated 4.8 years ago by Martin Morgan 25k • written 4.8 years ago by pavan-bioconductor • 0

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ExperimentData Deprecation Software Release Workflow

2.5 years ago • updated 2.0 years ago shepherl 3.8k

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