Bioconductor GAGE package

Showing : GAGE package • reset

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gage package gage

6.5 years ago melkile26 • 0

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gage gage package gene expression matrix gene set analysis

6.5 years ago atakanekiz ▴ 30

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3.1k

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gage package error

updated 6.7 years ago by James W. MacDonald 67k • written 6.7 years ago by Miskey, Csaba ▴ 20

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gage gage package pathview rna-seq

updated 2.9 years ago by Helen • 0 • written 6.9 years ago by tarun2 • 0

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2.2k

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kegg geneset genelist gage package

updated 7.4 years ago by Gordon Smyth 52k • written 7.4 years ago by sup230 ▴ 30

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1.6k

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gage package deseq2

7.5 years ago sup230 ▴ 30

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1.8k

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gage gage package

updated 8.2 years ago by Luo Weijun ★ 1.6k • written 8.3 years ago by Michael • 0

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R gage package rnaseq pathview

8.4 years ago joanito.liberti • 0

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gage package path.ids RNA-Seq

8.5 years ago rl1385 • 0

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1.1k

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t-test GAGE package Kolmogorov-Smirnov test Gene-Set enrichment

8.6 years ago smt8n • 0

10 results • Page 1 of 1

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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…

Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k

Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…

Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0

Thank you so much ! It's working !

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k

Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…

Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k

Thanks @fep29! ^^

Votes

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

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Popular Question to Robert Castelo ★ 3.4k

Popular Question to Robert Ivanek ▴ 750