Bioconductor Vranges

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881

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somaticsignatures vranges readvcfasvranges

6.3 years ago guillaume.dachy • 0

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2.0k

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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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1.4k

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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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1.9k

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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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1.5k

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vranges vcf to vranges

8.0 years ago Bogdan ▴ 670

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2.1k

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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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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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2.4k

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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

9.8 years ago summerela • 0

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3.4k

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variantannotation granges DNAStringSetList findoverlaps Vranges

9.8 years ago summerela • 0

10 results • Page 1 of 1

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Comment: Cross-validation with multiple control subgroups in limma by Ali Barry ▴ 40

Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …

Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k

limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…

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

Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…

Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60

Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…

Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k

For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…

Votes

C: edgeR and lack of counts ID on CPM matrix

A: DESeq2 Following RSEM

A: importing RSEM data into DESeq2

A: Expected counts from RSEM in DESeq2

A: Using RSEM reads for DESeq2

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