Bioconductor VRanges

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somaticsignatures vranges readvcfasvranges

6.2 years ago guillaume.dachy • 0

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variantannotation vcf readvcf vranges

updated 6.4 years ago by Michael Lawrence ★ 11k • written 6.4 years ago by david.mas • 0

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variantannotation VRanges R Rle

updated 6.4 years ago by Valerie Obenchain ★ 6.8k • written 6.4 years ago by Jayendra Shinde • 0

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1.9k

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somaticsignatures somaticsignatures package readvcfasvranges vranges

7.3 years ago • updated 7.2 years ago guillaume.dachy • 0

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vranges vcf to vranges

7.9 years ago Bogdan ▴ 670

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somaticsignatures vranges

updated 8.4 years ago by Julian Gehring ★ 1.3k • written 8.4 years ago by arsala521 ▴ 10

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1.7k

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granges vranges readvcfasvranges somaticsignatures

updated 8.7 years ago by Michael Lawrence ★ 11k • written 8.7 years ago by jpluta26 • 0

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SomaticSignatures mutationContext VRanges

updated 9.2 years ago by Julian Gehring ★ 1.3k • written 9.2 years ago by tesa.severson ▴ 10

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2.5k

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variantannotation vranges readvcf readvcfasvranges metadata

9.8 years ago summerela • 0

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variantannotation granges DNAStringSetList findoverlaps Vranges

9.8 years ago summerela • 0

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Comment: Help with RSEM counts: do I transpose matrix? by NB • 0

OK thank you.

Comment: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k

You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.

Comment: Help with RSEM counts: do I transpose matrix? by NB • 0

Thank you. If I have questions about QC/normalization, do I ask them here or ask a new question?

Answer: Help with RSEM counts: do I transpose matrix? by James W. MacDonald 67k

Yes. Samples in columns and genes in rows.

Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac ( by James W. MacDonald 67k

It's not informative except for me to say I was right that it's `getSeq` that is providing the error. It appears that `AddMotifs` is passin…

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Answer: Detecting genomic signatures of drug resistance breast cancer in transcriptom

Comment: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (

Answer: Issues with BSgenome.Mmusculus.UCSC.mm39 and generating motif matrix in Signac (

Comment: does anyone how to create rarefaction curves from a phyloseq object?

Answer: ANOVA like approach of edgeR

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