Bioconductor Reactome.db

Showing : reactome.db • reset

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reactome.db ReactomePA

2.6 years ago florianjt • 0

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2.0k

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reactome.db Bioconductor BiocManager

updated 2.9 years ago by Martin Morgan 25k • written 2.9 years ago by Michael Steinbaugh ▴ 90

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1.6k

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reactomepa reactomepa reactome bioconductor viewpathway reactome.db reactome

5.3 years ago martin.busch • 0

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1.5k

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reactomepa reactome.db reactome proteomics uniprot accessions

updated 5.9 years ago by willem.ligtenberg ▴ 150 • written 5.9 years ago by Miguel.Cosenza ▴ 10

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903

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reactome.db

updated 6.2 years ago by alserg ▴ 240 • written 6.2 years ago by Lluís Revilla Sancho ▴ 720

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reactome.db bioclite

6.4 years ago Jan-Jaap • 0

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reactome.db fgsea

updated 6.4 years ago by willem.ligtenberg ▴ 150 • written 6.4 years ago by alserg ▴ 240

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1.9k

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reactome.db

6.6 years ago Lluís Revilla Sancho ▴ 720

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1.2k

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reactome.db rsqlite

updated 6.7 years ago by willem.ligtenberg ▴ 150 • written 6.7 years ago by Lluís Revilla Sancho ▴ 720

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1.4k

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annotationdbi reactome.db bug

updated 6.8 years ago by Martin Morgan 25k • written 6.8 years ago by Lluís Revilla Sancho ▴ 720

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reactome.db annotation pathways

6.9 years ago Guido Hooiveld ★ 3.7k

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2.1k

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biomart reactome reactome.db id

updated 7.9 years ago by James W. MacDonald 63k • written 7.9 years ago by enricoferrero ▴ 660

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reactome.db

updated 8.1 years ago by willem.ligtenberg ▴ 150 • written 8.1 years ago by petyuk ▴ 70

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3.3k

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genesetenrichment pathways reactome.db

updated 8.5 years ago by willem.ligtenberg ▴ 150 • written 8.9 years ago by Guangchuang Yu ★ 1.2k

14 results • Page 1 of 1

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Comment: Suggested package missing from Development version of Bioconductor by shepherl 3.5k

Have you tried reaching out to the maintainers? If they do not fix the package it will remain unavailable and cause ERROR in your package.…

Answer: Batch effect adjust in model matrix by ATpoint ★ 3.4k

Each sample is a different day, that is called "nested", so there is nothing you can do here. Next time do a better experimental design, he…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

Oh, I see. If you can't use counts + offset then I prefer lengthScaledTPM to DESeq2, i.e. `txi$counts` to `DESeqDataSetFromMatrix()`. So …

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Christian • 0

I´m sorry causing confusion here, but the gene matrices I refer to are actually obtained via https://nf-co.re/rnaseq. The problem with the…

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts? by Michael Love 40k

For the reasons outlined in the Soneson paper, I'd prefer this pipeline: https://nf-co.re/rnaseq You cannot use these scaled TPM approach…

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Comment: Batch correction and repeated measures

batch effect : comBat or blocking in limma ?

Batch correction and repeated measures

Comment: Does countsFromAbundance="lengthScaledTPM" produce un-normalized counts?

Comment: Phenotype effect - building a contrast matrix - grouping vs interaction

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