Bioconductor VariantFiltering

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VariantAnnotation VariantFiltering

13 months ago Bogdan ▴ 670

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VariantFiltering

updated 16 months ago by Robert Castelo ★ 3.4k • written 16 months ago by Andrew Beggs ▴ 90

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RNAseq123 VariantFiltering Alignment VariantAnnotation

updated 2.0 years ago by James W. MacDonald 67k • written 2.0 years ago by Mohamed ▴ 30

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bioconductor variantfiltering

7.2 years ago Claus.Hultschig • 0

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variantannotation variantfiltering

updated 7.6 years ago by Michael Lawrence ★ 11k • written 7.6 years ago by Bogdan ▴ 670

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VariantFiltering

9.3 years ago claire.simpson • 0

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sequencing transcription variantfiltering annotation News

9.4 years ago Matthew Ritchie ▴ 1000

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variantfiltering phastcons

updated 9.6 years ago by Robert Castelo ★ 3.4k • written 9.6 years ago by Stefanie Tauber ▴ 40

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VariantFiltering VariantFiltering

10.5 years ago Robert Castelo ★ 3.4k

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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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