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4.9k

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clusterProfiler AnnotationHub GO uniprot

updated 10 weeks ago by Guido Hooiveld ★ 3.9k • written 3.2 years ago by Alberto • 0

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3.7k

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clusterProfiler GO GO enrichment genesetenrichment

updated 29 days ago by jandrade • 0 • written 6.3 years ago by Huang, Lei [BSD] - CRI ▴ 20

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599

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GO biomaRt

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

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525

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GO ensembldb

6 months ago • updated 5 months ago Rockbar • 0

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403

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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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348

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GO EnrichmentBrowser

updated 11 weeks ago by James W. MacDonald 65k • written 11 weeks ago by prity6459 • 0

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326

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GO limma CAMERA

updated 9 weeks ago by Gordon Smyth 50k • written 9 weeks ago by Tyler Sagendorf ▴ 10

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225

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DNAMethylation GO MethylationArray missMethyl EPICv2

updated 6 weeks ago by belinda.phipson ▴ 40 • written 6 weeks ago by s.malik • 0

8 results • Page 1 of 1

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Comment: Estimating Cell Counts for EPIC V2 array data by normawiedman059 • 0

0 [103] spam_2.9-1 doParallel_1.0.17 iterators_1.0.14 [106] foreach_1.5.2 beeswarm_0.4.0 tgp_2.4-20 [109] beanplot_1.3.1 fpc_2.2-9 dbscan_1…

Comment: Finding DEGs by using edgeR by Gordon Smyth 50k

Filtering (removing lowly expressed genes) is separate to normalization. It isn't clear why not subsetting would cause any difficulty. It …

Comment: How to make DGEList and design matrix by edgeR package by prity6459 • 0

Thank you for your suggestion. Yes, I have made DGEList and design matrix in my script. But I was not entirely confident while making thos…

Comment: Finding DEGs by using edgeR by prity6459 • 0

Hello Gordon, Thanks for your response. By normalization, I meant that I have already removed lowly expressed genes from my count matrix. …

Answer: FilterByExpr low counts with small sample size by Gordon Smyth 50k

It doesn't seem to me that there is necessarily any problem with the analysis. You say that there are "too many low-reads" but actually th…

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How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

Comment: DEXSeq DEXSeqDataSet count matrix duplication

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