Bioconductor LocateVariants

Showing : locateVariants • reset

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MetID TxDB.Hsapiens.UCSC.hg38.knownGene locateVariants GenomicFeatures VariantAnnotation

2.9 years ago davidhillis • 0

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969

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genomiclocation canonicaltranscripts locateVariants

updated 4.4 years ago by James W. MacDonald 68k • written 4.4 years ago by Paola • 0

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2.1k

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variantannotation locatevariants metadata mcols

updated 8.2 years ago by Valerie Obenchain ★ 6.8k • written 8.2 years ago by enricoferrero ▴ 680

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variantannotation predict coding locateVariants granges

8.3 years ago tony j • 0

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locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation

8.5 years ago Aleksandra • 0

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txdb.hsapiens.ucsc.hg19.knowngene ucsc annotation locatevariants variantannotation

updated 8.6 years ago by Valerie Obenchain ★ 6.8k • written 8.6 years ago by Lna • 0

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4.0k

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locatevariants variantannotation genomicfeatures

updated 9.3 years ago by Michael Lawrence ★ 11k • written 9.3 years ago by Lna • 0

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2.8k

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variantannotation locatevariants

10.5 years ago Jakob Goldmann • 0

8 results • Page 1 of 1

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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0

Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k

I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…

Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k

Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…

Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0

Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…

Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0

Hello, I was also wondering about the same issue. Did you figure it out?

Votes

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

Answer: Which preprocessing steps are needed before running limpa?

Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?

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Scholar to Gordon Smyth 53k

Popular Question to Peter Hickey ▴ 760