Bioconductor Pathway

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4.5k

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pathview KEGGgraph gage pathway pathway analysis

6.8 years ago • updated 6.7 years ago Luo Weijun ★ 1.6k

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1.5k

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deseq2 pathway ihw

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by guidobarzaghi ▴ 20

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1.7k

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pathview kegg r pathway

4.4 years ago AZ ▴ 30

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619

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pathway ORA limma CAMERA DGE

updated 8 months ago by Gordon Smyth 50k • written 8 months ago by manuelsokolov • 0

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1.0k

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limma pathway

updated 4.7 years ago by mikhael.manurung ▴ 270 • written 4.7 years ago by Dario Strbenac ★ 1.5k

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4.6k

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R ClusterProfiler Enrichment Pathway

updated 10 months ago by Guido Hooiveld ★ 3.9k • written 4.0 years ago by t.b.kuipers • 0

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1.1k

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pathway KEGG annotation annotationhub

updated 3.9 years ago by James W. MacDonald 65k • written 3.9 years ago by Bogdan ▴ 670

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1.4k

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pathway paxtools

9.5 years ago Guido Leoni ▴ 200

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726

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IHW deseq2 Pathway

updated 5.2 years ago by Michael Love 41k • written 5.2 years ago by guidobarzaghi ▴ 20

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896

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igraph miR2Pathway Pathway page_rank

updated 6.1 years ago by Martin Morgan 25k • written 6.1 years ago by genomic8328 ▴ 10

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910

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pathway SBGNview Reactome pathview PANTHER

written 3.1 years ago by Luo Weijun ★ 1.6k

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967

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pathway KEGGREST GSEA

updated 3.1 years ago by Kevin Blighe ★ 3.9k • written 3.1 years ago by MOHAMMAD • 0

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771

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kegg pathway pathview

5.1 years ago Ahdee ▴ 50

13 results • Page 1 of 1

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Comment: DESeq2 output used for PCA plot on R studio by Aaliya • 0

How am i making the data? I am using the DESeq2 output data which I had generated

Answer: Use of negative binomial model for exponential decay rate estimation using DESeq by Michael Love 41k

Sounds reasonable. For ranking genes, you could choose those with low decay rate but removing thoses where it is indistinguishable from …

Answer: Citation for edgeR user guide by Gordon Smyth 50k

Thanks for thinking about how to cite edgeR. Citations are indeed the main way by which the edgeR authors get credit for their work. The Us…

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You are just making up data? What is the point of this exercise?

Comment: How to retrieve gene ontology GO class? by James W. MacDonald 65k

What do you mean by 'the information'? Do you have things in particular that you want?

Votes

Answer: Citation for edgeR user guide

Use of negative binomial model for exponential decay rate estimation using DESeq (or similar)

Answer: How to correct for age, sex, etc. from an RNA-seq data in DESeq2.

Answer: minfi::read.metharray.exp

Comment: Trying to use enrichGO

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