Bioconductor LocateVariants

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

22 months ago davidhillis • 0

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793

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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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1.7k

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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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1.3k

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variantannotation predict coding locateVariants granges

7.3 years ago tony j • 0

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locatevariants txdb.hsapiens.ucsc.hg19.knowngene variantannotation

7.5 years ago Aleksandra • 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

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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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2.4k

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variantannotation locatevariants

9.4 years ago Jakob Goldmann • 0

8 results • Page 1 of 1

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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k

FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

I see. Thank you ATpoint!

Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0

Thanks James!

Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k

I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…

Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10

Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…

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Comment: can't install tscR

Answer: Csaw normalization strategies - general inquiry

A: DESeq2 interaction term

Comment: Recount3 data correspond to TCGA data

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