Bioconductor KEGGgraph

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igraph KEGGgraph RCy3 GraphNEL

3 months ago • updated 8 weeks ago Arindam ▴ 80

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625

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KEGGgraph KEGG

updated 6 months ago by Guido Hooiveld ★ 4.1k • written 6 months ago by Fara • 0

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KEGGgraph org.Cs.eg.db clusterProfiler KEGG AnnotationHubSoftware

updated 7 months ago by James W. MacDonald 67k • written 7 months ago by fernanda.backsouza ▴ 30

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526

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KEGGREST GenomicDistributionsData KEGGgraph KEGG

updated 7 months ago by Guido Hooiveld ★ 4.1k • written 7 months ago by fernanda.backsouza ▴ 30

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enrichKEGG KEGGgraph KEGG

updated 9 months ago by Guido Hooiveld ★ 4.1k • written 10 months ago by cinzia.spagnoli • 0

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Answer: Cannot install GO.db and org.Hs.eg.db by James W. MacDonald 67k

You might try tracing the namespace loading. ``` Sys.setenv("_R_TRACE_LOADNAMESPACE_"="2") install("org.Hs.eg.db") ``` And see if th…

Answer: p value is 0, padj is 0 by James W. MacDonald 67k

It is quite possible for a very small p-value to remain very small after multiplicity adjustment. I don't know the cutoff for `DESeq2` to r…

Answer: Help using rtracklayer for gene ID extraction by James W. MacDonald 67k

You don't need `rtracklayer` for this (not directly anyway), but instead you need `txdbmaker` which you can use to make a `TxDb` object tha…

Answer: Feature Counts - potential bug with outfile.jcounts by Wei Shi ★ 3.6k

We will further develop the junction quantification module to support the use of user-provided annotation data for annotating detected junc…

Comment: Pre-filtering TPM kallisto for ssGSEA / DESeq2 by georgii.vdovin • 0

Thank you!

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Answer: Feature Counts - potential bug with outfile.jcounts

Answer: Pre-filtering TPM kallisto for ssGSEA / DESeq2

Answer: Mapping Between GenBank ID's and Uniprot

Comment: What type of counts data to import for performing Isoform analysis in edgeR

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