Bioconductor Organismdb

Showing : organismdb • reset

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1.6k

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OrganismDb AnnotationForge

5 months ago Ozan • 0

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1.7k

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clusterProfiler OrganismDb

updated 11 months ago by Guido Hooiveld ★ 4.1k • written 11 months ago by Aastha Kapoor • 0

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AnnotationForge OrganismData OrganismDb

17 months ago abhisek001 • 0

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annotation organismdb

updated 8.2 years ago by Martin Morgan 25k • written 8.2 years ago by Guido Hooiveld ★ 4.1k

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annotationhub organismdb orgdb unsupported organisms

updated 8.8 years ago by Valerie Obenchain ★ 6.8k • written 8.8 years ago by Guido Hooiveld ★ 4.1k

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promoter granges refseq ucsc organismdb

updated 9.0 years ago by Robert Castelo ★ 3.4k • written 9.0 years ago by efoss ▴ 10

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GO OrganismDb ggbio GO OrganismDb ggbio

updated 10.0 years ago by dalloliogm ▴ 50 • written 10.3 years ago by Georg Otto ▴ 120

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annotationdbi annotation organismdb loadnamespace

10.0 years ago milorobertsmith • 0

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go annotation organismdb

updated 10.1 years ago by James W. MacDonald 67k • written 10.1 years ago by Guido Hooiveld ★ 4.1k

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organismdb annotationdbi annotationforge

updated 10.2 years ago by Marc Carlson ★ 7.2k • written 10.2 years ago by artur ▴ 80

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Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome MEDIPS

updated 10.9 years ago by Matthias Lienhard ▴ 280 • written 10.9 years ago by Hervé Pagès 16k

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Annotation GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome GO

11.0 years ago Hervé Pagès 16k

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GO Cancer BSgenome OrganismDb SNPlocs TranscriptDb Biostrings BSgenome rtracklayer MEDIPS

11.0 years ago Hervé Pagès 16k

13 results • Page 1 of 1

Recent ...

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Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k

I'm adding my comment to the threaded section ... I don't have any suggestions here but whatever method you're using is not appropriate up…

Comment: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

If you do it this way, the dispersion estimates would be much higher than they should (as the cell type difference is not accounted for in …

Comment: ANOVA like approach of edgeR by SamGG ▴ 350

Simply remove the cell type from the model. design <- model.matrix(~targets$Status)

Answer: ANOVA like approach of edgeR by Yunshun Chen ▴ 880

You could try the followings: > design <- model.matrix(~ 0 + group) > contrast <- makeContrasts(PvsL = 0.5*(L.pregnant + B.pregnan…

Answer: Identical samples after deseq2 batch effect removal by maripane • 0

Thanks Michael, so is there a way to work around this issue? Can I somehow make sure I can remove this batch effects without overcorrecti…

Votes

Answer: ANOVA like approach of edgeR

A: ANOVA-like test with edgeR

Answer: CleanUpRNAseq with a GTF that is missing mitochondria annotation data

A: TopGO: How to retrieve the gene list related to a GO ID ?

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