Bioconductor Gene annotation

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biomaRt gene annotation

updated 4.7 years ago by James W. MacDonald 67k • written 4.7 years ago by jnaviapelaez ▴ 10

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1.3k

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R ensemblVEP gene annotation Variant Effect Predictor Ensembl VEP

5.3 years ago ycchang • 0

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1.6k

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recount RNAseq gencode lncRNA gene annotation

updated 5.6 years ago by chris.wilks ▴ 70 • written 5.6 years ago by francesco.gandolfi ▴ 20

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4.0k

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edger DGEList org.hs.eg.db gene annotation

updated 3.1 years ago by IIart.hubII • 0 • written 6.9 years ago by svlachavas ▴ 830

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1.5k

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gene ontology goslim enrichment analysis gene annotation

8.6 years ago mirko • 0

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Answer: Is it possible to parallelise saveHDF5SummarizedExperiment by Hervé Pagès 16k

Hi Stefano, Unfortunately HDF5 doesn't support concurrent writing so parallelising is not an option. A few things that maybe could help: …

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

It's a simple two-liner in [getsrc.sh][1] ``` awk -F'\t' 'BEGIN {OFS=FS} {if($3 != $11 && $11 != "-") $3 = $11; print $0}' gene_info > tmp…

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by Guido Hooiveld ★ 4.1k

Thanks for changing this! Just to confirm I understood it correctly: the `Symbol` will (still) be used, and will be replaced by `Symbol fro…

Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db? by James W. MacDonald 67k

OK, there are 157 MT genes in maybe 6 species for which the symbols are not correct, and I added code to swap the 'Symbol from nomenclature…

Comment: Tximport with RSEM error by Michael Love 42k

Would you post a new issue with example code and maybe what the files look like?

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Comment: incomplete official symbol mitochondrial genes in org.Hs.eg.db?

Answer: Supercells with Basilisk fails for dtype('float64') to dtype('int64') conversion

A: GOseq analysis with only upregulated or downregulated genes

Answer: Properly constructing a hypergeometric test

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