Bioconductor Gsealm

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Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR

12.1 years ago Malcolm Cook ★ 1.6k

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2.6k

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Network limma GOstats GSEAlm edgeR ReportingTools Network limma GOstats GSEAlm edgeR

updated 12.1 years ago by Malcolm Cook ★ 1.6k • written 12.1 years ago by Josh Kaminker ▴ 20

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biomaRt GSEAlm biomaRt GSEAlm

updated 12.6 years ago by James W. MacDonald 67k • written 12.6 years ago by b1gorsuch@comcast.net ▴ 20

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910

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GSEAlm GSEAlm

16.1 years ago Mark W Kimpel ▴ 830

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1.5k

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GO GSEAlm GO GSEAlm

updated 16.2 years ago by rgentleman ★ 5.5k • written 16.2 years ago by Mark W Kimpel ▴ 830

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GO affy goTools Category GSEABase GSEAlm GO affy goTools Category GSEABase GSEAlm

updated 16.2 years ago by Dykema, Karl ▴ 90 • written 16.2 years ago by Mark W Kimpel ▴ 830

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763

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GSEAlm GSEAlm

16.7 years ago Assaf Oron ▴ 40

7 results • Page 1 of 1

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Answer: I am having issues with bowtie2_build by James W. MacDonald 67k

Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…

Answer: DEG analysis across multiple timepoints, treatments and tissues by Michael Love 43k

Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…

Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

Thanks James!

Votes

Answer: Unable to install nloptr

Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?

C: How does edgeR cpm function calculate log(CPM) values?

Answer: Selection of correct coefficients or contrasts in DESeq2

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