Bioconductor Aracne

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grndata GRN ARACNE WGCNA

2.4 years ago Harrsha • 0

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viper aracne regulatory network aracne.networks

8.2 years ago ldetorrente ▴ 10

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Comment: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k

`keepStandardChromosomes()` is not smart enough to know what to keep for this assembly. Note that what `keepStandardChromosomes()` means by…

Comment: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k

Thanks Hervé! Very helpful. However, I believe that `keepStandardChromosomes` gets called by `gDNAx`, and it appears not to work correctly.…

Answer: nightmare to make custom txdb for genomes from ToxoDB by Hervé Pagès 16k

Is this for genome assembly TGA4? https://www.ncbi.nlm.nih.gov/datasets/genome/GCF_000006565.2/ If that's the case then: ``` library(t…

Answer: nightmare to make custom txdb for genomes from ToxoDB by James W. MacDonald 67k

Your post title is misleading. You have no problem whatsoever generating the `TxDb`, the problem is using it with `gDNAx`, which attempts t…

Answer: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k

Just fit a model `~condition + experiment` where `condition` has three levels A, B and C. Ideally, use limma and include duplicate correlat…

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