Bioconductor Locatevariants

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

22 months ago davidhillis • 0

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1.7k

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variantannotation locatevariants metadata mcols

updated 7.1 years ago by Valerie Obenchain ★ 6.8k • written 7.1 years ago by enricoferrero ▴ 660

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variantannotation locatevariants

9.4 years ago Jakob Goldmann • 0

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2.9k

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locatevariants variantannotation genomicfeatures

updated 8.2 years ago by Michael Lawrence ★ 11k • written 8.2 years ago by Lna • 0

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variantannotation predict coding locateVariants granges

7.3 years ago tony j • 0

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1.8k

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locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation

7.4 years ago Aleksandra • 0

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791

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genomiclocation canonicaltranscripts locateVariants

updated 3.4 years ago by James W. MacDonald 67k • written 3.4 years ago by Paola • 0

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1.6k

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

updated 7.6 years ago by Valerie Obenchain ★ 6.8k • written 7.6 years ago by Lna • 0

8 results • Page 1 of 1

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Answer: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k

Following the discussion of this post, the package [gDNAx](https://bioconductor.org/packages/gDNAx) has been fixed in devel and release 1.4…

Answer: Selection of correct coefficients or contrasts in DESeq2 by James W. MacDonald 67k

Using R's model formulation for three-way interactions is probably not the way to go here. Or at least I wouldn't do it that way. An easier…

Comment: How to generate circular cnetplot and color nodes and edges in the same plot ? by Blandine • 0

Thank you so much ! It's working !

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by James W. MacDonald 67k

Yes. If you have the Illumina IDs, then all the annotation data that `cpg.annotate` uses will be based on hg19. It doesn't matter if TCGA l…

Comment: Recount3 data correspond to TCGA data by Leonardo Collado Torres ★ 1.1k

Thanks @fep29! ^^

Votes

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

Answer: DESeq2- merging technical vs biological replicates

Answer: SingleCellExperiment convenience function for metadata+expression?

How to correct for tumor purity using DESeq2 to analyze TCGA tumor sample expression.

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Popular Question to Robert Castelo ★ 3.4k

Popular Question to Robert Ivanek ▴ 750