Bioconductor VRanges

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somaticsignatures vranges readvcfasvranges

6.3 years ago guillaume.dachy • 0

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variantannotation vcf readvcf vranges

updated 6.5 years ago by Michael Lawrence ★ 11k • written 6.5 years ago by david.mas • 0

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variantannotation VRanges R Rle

updated 6.5 years ago by Valerie Obenchain ★ 6.8k • written 6.5 years ago by Jayendra Shinde • 0

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somaticsignatures somaticsignatures package readvcfasvranges vranges

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

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vranges vcf to vranges

8.0 years ago Bogdan ▴ 670

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somaticsignatures vranges

updated 8.5 years ago by Julian Gehring ★ 1.3k • written 8.5 years ago by arsala521 ▴ 10

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granges vranges readvcfasvranges somaticsignatures

updated 8.8 years ago by Michael Lawrence ★ 11k • written 8.8 years ago by jpluta26 • 0

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SomaticSignatures mutationContext VRanges

updated 9.3 years ago by Julian Gehring ★ 1.3k • written 9.3 years ago by tesa.severson ▴ 10

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2.6k

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variantannotation vranges readvcf readvcfasvranges metadata

9.9 years ago summerela • 0

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variantannotation granges DNAStringSetList findoverlaps Vranges

9.9 years ago summerela • 0

10 results • Page 1 of 1

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Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Gordon Smyth 52k

Follow the vignette. It explains how to call edgeR's cpm function to use the offsets.

Comment: edgeR + tximport: calcNormFactors and the usage of offsets by Andre • 0

But if i want to do another type of analysis like Wilcoxon/Mann-Whitney and want to incorporate salmon offset can i simply use the cpm func…

Comment: DESeq error: counts matrix should be numeric, currently it has mode: character by Kucsera • 0

After applying your suggestion, the following error pops up: ``` Error in mde(x) : 'list' object cannot be coerced to type 'double' ```

Answer: DESeq error: counts matrix should be numeric, currently it has mode: character by ATpoint ★ 4.6k

R thinks your data are characters (e.g. "1", "2", instead of 1, 2) so given that your `counts_data` indeed only contains counts, do: `mo…

Comment: Any tools to convert .gff to .gtf format by ControlF5 • 0

Yes, the Appsierra team recently built a tool to convert .gff to .gtf format. [ControlF5][1] is providing the best software testing service…

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A: GWAS analysis with Illumina HumanOmni5-4 BeadChip - recommended software and wor

A: RNA-seq Normalisation - normalise all samples in experiment or only the ones use

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?

Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio

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