Bioconductor Hub genes

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WGCNA eigengene hub genes

7.2 years ago yifangt ▴ 20

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wgcna rbgl graph coexpression hub genes

updated 8.8 years ago by Peter Langfelder ★ 3.0k • written 8.8 years ago by Alan Smith ▴ 150

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wgcna visant module hub genes

updated 8.9 years ago by etycksen • 0 • written 8.9 years ago by agattorosso • 0

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4

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WGCNA Hub Genes KmE Intramodular Connectivity

updated 9.5 years ago by Peter Langfelder ★ 3.0k • written 9.6 years ago by brohawndg ▴ 150

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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!

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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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