Bioconductor Pathway

Showing : pathway • reset

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4.5k

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pathview KEGGgraph gage pathway pathway analysis

6.8 years ago Luo Weijun ★ 1.6k

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1.4k

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pathway paxtools

9.5 years ago Guido Leoni ▴ 200

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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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731

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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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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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1.7k

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pathview kegg r pathway

4.5 years ago • updated 4.4 years ago AZ ▴ 30

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4.7k

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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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979

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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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641

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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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905

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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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923

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pathway SBGNview Reactome pathview PANTHER

written 3.1 years ago by Luo Weijun ★ 1.6k

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780

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kegg pathway pathview

5.2 years ago Ahdee ▴ 50

13 results • Page 1 of 1

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Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0

Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …

Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k

Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k

I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …

Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k

It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…

Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k

This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…

Votes

Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-

Answer: limma Intercept vs No-intercept models completely changing DMR results?

Answer: CombineArrays for EPIC and EPIC V2

Answer: Too many significant genes when integrating gtex and tcga

Comment: Too many significant genes when integrating gtex and tcga

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