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5.1k

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clusterProfiler AnnotationHub GO uniprot

updated 3 months ago by Guido Hooiveld ★ 4.0k • written 3.3 years ago by Alberto • 0

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3.8k

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clusterProfiler GO GO enrichment genesetenrichment

updated 8 weeks ago by jandrade • 0 • written 6.4 years ago by Huang, Lei [BSD] - CRI ▴ 20

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639

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GO biomaRt

updated 10 months ago by James W. MacDonald 66k • written 10 months ago by cstorer • 0

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593

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GO ensembldb

7 months ago Rockbar • 0

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472

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GO EnrichmentBrowser

updated 3 months ago by James W. MacDonald 66k • written 3 months ago by prity6459 • 0

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441

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go DESeq2

updated 8 months ago by James W. MacDonald 66k • written 8 months ago by Alvin • 0

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393

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GO limma CAMERA

updated 3 months ago by Gordon Smyth 50k • written 3 months ago by Tyler Sagendorf ▴ 10

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295

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DNAMethylation GO MethylationArray missMethyl EPICv2

updated 11 weeks ago by belinda.phipson ▴ 40 • written 11 weeks ago by s.malik • 0

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GO KEGG gage pathview

5 days ago danalvoronov ▴ 10

9 results • Page 1 of 1

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Comment: ChAMP installation issue by Tahirah • 0

Hello. Could you please share how you managed to install ChAMP in R 4.4.0? I also have R 4.4.0 and Bioconductor 3.19 version and ChAMP fail…

Answer: Identifying DEGs using limma - NanoString GeoMx-NGS RNA Expression Data by James W. MacDonald 66k

Yes, you can use `limma`.

Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k

You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…

Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k

If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …

Comment: Help with ENmix readidat by James W. MacDonald 66k

Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …

Votes

how to control age and gender effect in expression data using DESeq2

Answer: Error retrieving ensembl gene id using biomaRt...

Comment: LRT, more than two conditions and pairwise comparisons

Answer: Control group between 2 batches have different expression in RNAseq data

Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?

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Scholar to Mike Smith ★ 6.5k

Popular Question to mohammedtoufiq91 ▴ 10