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3.7k

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clusterProfiler GO GO enrichment genesetenrichment

updated 5 weeks ago by jandrade • 0 • written 6.4 years ago by Huang, Lei [BSD] - CRI ▴ 20

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4.9k

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clusterProfiler AnnotationHub GO uniprot

updated 11 weeks ago by Guido Hooiveld ★ 3.9k • written 3.2 years ago by Alberto • 0

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332

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GO limma CAMERA

updated 10 weeks ago by Gordon Smyth 50k • written 10 weeks ago by Tyler Sagendorf ▴ 10

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411

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go DESeq2

updated 7 months ago by James W. MacDonald 65k • written 7 months ago by Alvin • 0

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541

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GO ensembldb

6 months ago Rockbar • 0

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360

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GO EnrichmentBrowser

updated 12 weeks ago by James W. MacDonald 65k • written 12 weeks ago by prity6459 • 0

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235

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DNAMethylation GO MethylationArray missMethyl EPICv2

updated 7 weeks ago by belinda.phipson ▴ 40 • written 7 weeks ago by s.malik • 0

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606

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GO biomaRt

updated 9 months ago by James W. MacDonald 65k • written 9 months ago by cstorer • 0

8 results • Page 1 of 1

Recent ...

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Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k

You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…

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…

Votes

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq

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

Awards • All

Scholar to James W. MacDonald 65k

Supporter to JKim • 0