Bioconductor VRanges

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somaticsignatures vranges readvcfasvranges

7.2 years ago guillaume.dachy • 0

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variantannotation vcf readvcf vranges

updated 7.3 years ago by Michael Lawrence ★ 11k • written 7.3 years ago by david.mas • 0

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variantannotation VRanges R Rle

updated 7.4 years ago by Valerie Obenchain ★ 6.8k • written 7.4 years ago by Jayendra Shinde • 0

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somaticsignatures somaticsignatures package readvcfasvranges vranges

8.2 years ago • updated 8.1 years ago guillaume.dachy • 0

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vranges vcf to vranges

8.8 years ago Bogdan ▴ 670

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somaticsignatures vranges

updated 9.4 years ago by Julian Gehring ★ 1.3k • written 9.4 years ago by arsala521 ▴ 10

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granges vranges readvcfasvranges somaticsignatures

updated 9.6 years ago by Michael Lawrence ★ 11k • written 9.6 years ago by jpluta26 • 0

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SomaticSignatures mutationContext VRanges

updated 10.2 years ago by Julian Gehring ★ 1.3k • written 10.2 years ago by tesa.severson ▴ 10

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variantannotation vranges readvcf readvcfasvranges metadata

10.7 years ago summerela • 0

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variantannotation granges DNAStringSetList findoverlaps Vranges

10.7 years ago summerela • 0

10 results • Page 1 of 1

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Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

Comment: deseq2 filter the low counts by empty_mt • 0

Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…

Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0

That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…

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Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

Answer: Important: Bioconductor Release 3.22 Delayed

A: Multi-level experiments in Limma

Answer: Should voomWithQualityWeights still be used when the sample-specific weights var

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