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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…
Comment: Error in get_anno_data(ontology) : ontology not supported yet... by GODseeker • 0
thank u so much ,god bless u,my dear friend.
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Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
Comment: Feature Counts - potential bug with outfile.jcounts
Answer: Feature Counts - potential bug with outfile.jcounts
Comment: Can we get beta values with DMRcate package
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