Bioconductor Sushi

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R sushi

updated 8.2 years ago by dphansti ▴ 10 • written 8.3 years ago by javier.mendoza • 0

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sushi

updated 8.6 years ago by Steve Lianoglou ★ 13k • written 8.6 years ago by Bogdan ▴ 670

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sushi plotBed data.frame

8.0 years ago waqasnayab • 0

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sushi plotBed

updated 8.1 years ago by dphansti ▴ 10 • written 8.2 years ago by Dimitris Polychronopoulos ▴ 80

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sushi

7.6 years ago snamjoshi87 ▴ 40

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Sushi

updated 8.1 years ago by dphansti ▴ 10 • written 8.1 years ago by Till ▴ 30

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sushi bed

5.6 years ago maltethodberg ▴ 170

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sushi plotGenes

6.3 years ago portia.mcghan • 0

8 results • Page 1 of 1

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Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k

You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…

Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0

My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…

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…

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?

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0