User: zhang.jianhai

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Posts by zhang.jianhai

<prev • 53 results • page 1 of 6 • next >
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Comment: C: BiocCheck package size
... Ok, thanks for the reminder. ...
written 3 months ago by zhang.jianhai0
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BiocCheck package size
... Hello everyone, I am submitting an R package to Bioconductor. I have 2 vignettes and the size is 5.7M and 2.3M respectively. BiocCheck requires the package size is within 4M, so I cannot pass the check. The vignette size is so large since it contains many png images. I have reduced the resolution ...
bioccheck written 3 months ago by zhang.jianhai0 • updated 3 months ago by Hervé Pagès ♦♦ 14k
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Comment: C: Normalisation upstream rlog
... Can you share the link of the workflow that contains the transformation section? Regards. ...
written 4 months ago by zhang.jianhai0
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Normalisation upstream rlog
... Hello, In the RNA Seq count data, upstream rlog normalisation should there be other normalisations like RPKM, CPM, etc.? Or the rlog is directly applied on raw count data? Regards. ...
deseq2 rlog written 4 months ago by zhang.jianhai0 • updated 4 months ago by Michael Love24k
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Comment: C: KEGGREST mapping between genes and pathways
... I am working on locus IDs, to convert transcript ids to locus ids, should I replace "t" with "g" (based on your link, it seems yes)? ...
written 6 months ago by zhang.jianhai0
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clusterProfiler GeneRatio minGSSize
... Hello, I am using "enrichKEGG" on rice genes. The entriz ids are `entr <- c("4337100", "4336350", "4324731", "4336393", "4347034", "4345789", "4336561", "107276072", "4324047", "4352785", "4344600", "4327916", "4328844", "4336915", "4338072", "4339251", "4325336", " ...
enrichkegg generatio written 6 months ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... All the gene ids have a "t" (Os01t0118000) inside rather than a "g" (Os05g0532600). Why is that? ...
written 6 months ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... I see. Thank you very much for reply! ...
written 6 months ago by zhang.jianhai0
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Comment: C: KEGGREST mapping between genes and pathways
... It is very useful, but why there is "-01" or "-00" at the end of gene IDs (e.g. Os01t0191700-01)? ...
written 6 months ago by zhang.jianhai0
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KEGGREST mapping between genes and pathways
... Hello, I want to enrich KEGG pathways on my rice genes. I tried "clusterProfiler", but its input is entrezID and my gene ids are RAPIDs (Os02g0617800). I want to keep using the RAPIDs, so I have to write my own enrichment functions. To do this, I need the mapping between RAPIDs and pathways. How to ...
keggrest mapping genes to pathways written 6 months ago by zhang.jianhai0 • updated 6 months ago by Gordon Smyth38k

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