Bioconductor Pathway

Showing : pathway • reset

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613

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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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pathway SBGNview Reactome pathview PANTHER

written 3.1 years ago by Luo Weijun ★ 1.6k

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964

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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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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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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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1.7k

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pathview kegg r pathway

4.4 years ago AZ ▴ 30

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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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770

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kegg pathway pathview

5.1 years ago Ahdee ▴ 50

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721

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IHW deseq2 Pathway

updated 5.1 years ago by Michael Love 41k • written 5.1 years ago by guidobarzaghi ▴ 20

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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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894

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igraph miR2Pathway Pathway page_rank

updated 6.0 years ago by Martin Morgan 25k • written 6.0 years ago by genomic8328 ▴ 10

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4.4k

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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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1.4k

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pathway paxtools

9.5 years ago Guido Leoni ▴ 200

13 results • Page 1 of 1

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Comment: DESeq filtering specific to contrasts by Michael Love 41k

It will likely not filter it out, but really the per-dataset details would affect the results.

Comment: DESeq filtering specific to contrasts by Carlin95 • 0

Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…

Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10

Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0

Thank you very much for your reply! I will do so. Kind regards, Seyram

Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0

Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…

Votes

Install/Switch between multiple versions of R, Rstudio, and Bioconductor

A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

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

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