Bioconductor Rstudio

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Ensembl Rstudio ensembldb AnnotationHub ensdb

updated 6 weeks ago by shepherl 3.8k • written 2.2 years ago by jon.klonowski ▴ 40

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479

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Rstudio cDNA ensembldb NCBI

4 months ago R_Page • 0

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447

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AccNo OrgDb convert Organismname RStudio

updated 5 months ago by James W. MacDonald 65k • written 5 months ago by j_denton • 0

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1.5k

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error RStudio ggplot2 DESeq2

updated 5 months ago by James W. MacDonald 65k • written 5 months ago by BioES • 0

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754

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RStudio convert ensembldb NCBI

5 months ago j_denton • 0

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983

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scRNAseq RStudio DESeq2

updated 8 months ago by ATpoint ★ 4.0k • written 8 months ago by DrFizz • 0

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378

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Rstudio scRNAseq DESeq2

updated 8 months ago by ATpoint ★ 4.0k • written 8 months ago by DrFizz • 0

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338

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Rstudio plotPCA DESeq2

5 months ago • updated 4 months ago yee • 0

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224

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RStudio ggkegg

updated 4 months ago by James W. MacDonald 65k • written 4 months ago by Ramirj49 • 0

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180

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DESeq2 RSTUDIO PCAtools

updated 2 hours ago by swbarnes2 ★ 1.3k • written 1 day ago by Aaliya • 0

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