Bioconductor Vranges

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838

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somaticsignatures vranges readvcfasvranges

6.1 years ago guillaume.dachy • 0

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1.9k

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variantannotation vcf readvcf vranges

updated 6.3 years ago by Michael Lawrence ★ 11k • written 6.3 years ago by david.mas • 0

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1.3k

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variantannotation VRanges R Rle

updated 6.3 years ago by Valerie Obenchain ★ 6.8k • written 6.3 years ago by Jayendra Shinde • 0

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1.9k

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somaticsignatures somaticsignatures package readvcfasvranges vranges

7.2 years ago • updated 7.1 years ago guillaume.dachy • 0

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1.4k

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vranges vcf to vranges

7.7 years ago Bogdan ▴ 670

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somaticsignatures vranges

updated 8.3 years ago by Julian Gehring ★ 1.3k • written 8.3 years ago by arsala521 ▴ 10

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1.6k

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granges vranges readvcfasvranges somaticsignatures

updated 8.5 years ago by Michael Lawrence ★ 11k • written 8.5 years ago by jpluta26 • 0

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2.3k

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SomaticSignatures mutationContext VRanges

updated 9.1 years ago by Julian Gehring ★ 1.3k • written 9.1 years ago by tesa.severson ▴ 10

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variantannotation vranges readvcf readvcfasvranges metadata

9.6 years ago summerela • 0

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3.3k

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variantannotation granges DNAStringSetList findoverlaps Vranges

9.6 years ago summerela • 0

10 results • Page 1 of 1

Recent ...

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Answer: segfault when using singleR with Azimuth reference by James W. MacDonald 67k

The training step is usually faster than the classification step, so you might try running `trainSingleR` on the reference to see if that i…

Comment: Batch Effect in DESeq2, how to control, how to remove it, how to address biologi by James W. MacDonald 67k

You don't. I believe Fisher has a quote that applies here. Also, please don't add to five year old posts. Start a new one.

Comment: Convert HGVS Representation back to Reference Genome Coordinates by Vince Schulz ▴ 150

Not a bioconductor solution, and probably not easily code-able, but there is a batch validate/convert function available here: https://vari…

Answer: How to control batch effect if Group and batch are same? by ATpoint ★ 4.4k

You cannot do any correction. That's the simple and only answer. You cannot distinguish true biological effect from unwanted technical vari…

Comment: Batch Effect in DESeq2, how to control, how to remove it, how to address biologi by Bioinformagician • 0

How to control batch effect if Group and batch are same?. For example, I have all tumor samples from batch1 and all normal samples from bat…

Votes

Answer: How to control batch effect if Group and batch are same?

Comment: Normalization RNA-seq for multiple plates

Answer: How to control batch effect if Group and batch are same?

Answer: segfault when using singleR with Azimuth reference

Answer: How does Deseq2 deal with the row with zero when calculating size factors

Awards • All

Scholar to Ryan C. Thompson ★ 7.9k