Bioconductor Filtervcf

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2.9k

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variantannotation vcf readvcf filtervcf scanvcfparam

7.4 years ago Didi ▴ 10

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filtervcf

updated 7.9 years ago by Martin Morgan 25k • written 8.0 years ago by Bogdan ▴ 670

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filtervcf variantannotation

updated 8.1 years ago by Martin Morgan 25k • written 8.1 years ago by stephen sefick ▴ 60

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variantannotation filtervcf

updated 9.1 years ago by Michael Lawrence ★ 11k • written 9.1 years ago by TimothéeFlutre ▴ 80

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variantannotation vcf filtervcf

updated 9.2 years ago by Martin Morgan 25k • written 9.2 years ago by TimothéeFlutre ▴ 80

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variantannotation filtervcf vcf

updated 9.2 years ago by Michael Lawrence ★ 11k • written 9.2 years ago by TimothéeFlutre ▴ 80

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VariantAnnotation filterVcf ScanVcfParam vcf writeVcf

updated 9.4 years ago by Martin Morgan 25k • written 9.4 years ago by pau.puigdevall • 0

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VariantAnnotation filterVcf

9.4 years ago pau.puigdevall • 0

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2.3k

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variantannotation filterVcf readvcfasvranges filterRules

updated 9.8 years ago by Martin Morgan 25k • written 9.8 years ago by Sigve Nakken ▴ 50

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Answer: Error in get_anno_data(ontology) : ontology not supported yet... by Guido Hooiveld ★ 4.1k

Did you check the help page for the function `enrichDO`? Type `?enrichDO`. I am asking, because there it is stated that the argument `ont`…

Comment: Build error on kunpeng2 Linux aarch64 by martin.grigorov ▴ 10

Hi, There was a problem with `icu` and because of that the (r)curl library was not installed. The system/OS curl library is one version ol…

Answer: Standardization of rlog transformed counts before PCA by ATpoint ★ 4.6k

I guess you mean scaling in terms of Z-scoring? There are plenty of posts towards scaling in PCA both here on Bioconductor and in other com…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Also, re DMR.plot(), yes the understanding is that all DMRs from EPICv2 should be plotted in hg38. I've left that implied for the user sinc…

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200

Hi Xiaofei, Thanks for this. If your data is from 450K, you'll have to call your DMRs in hg19, and then lift the DMR ranges over to hg38 p…

Votes

Comment: Can we get beta values with DMRcate package

Answer: Can we get beta values with DMRcate package

DiffBind giving different results from dba.report() and dba.analyze(..., bRetrieveAnalysis=TRUE)

Answer: Deseq2 Design

Answer: Fold change calculation in Diffbind vs. DESEQ2?

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Scholar to James W. MacDonald 67k