Bioconductor ScanVcfParam

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VariantAnnotation subset ScanVcfParam

updated 5.0 years ago by Martin Morgan 25k • written 5.0 years ago by Dario Strbenac ★ 1.6k

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variantannotation vcf readvcf filtervcf scanvcfparam

7.7 years ago Didi ▴ 10

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R variantannotation vcf scanvcfparam readvcf

updated 8.8 years ago by Michael Lawrence ★ 11k • written 8.8 years ago by emily.mccann • 0

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VariantAnnotation filterVcf ScanVcfParam vcf writeVcf

updated 9.7 years ago by Martin Morgan 25k • written 9.7 years ago by pau.puigdevall • 0

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Answer: Model performance for spline modelling of RNA-seq timecourses in edgeR by Gordon Smyth 52k

I don't understand your question, because there is no difference between limma or glmFit or glmQLFit in terms of spline modeling or the tes…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

Perhaps edgeR's upperquartile normalization handles this better, the MA looks a lot more centered at 0 ![enter image description here][1]…

Answer: DESeq2 - am I extracting results incorrectly? by James W. MacDonald 68k

If I assume that Followup gets converted to T3 and Treatment to LowSug somewhere along the line (and therefore GroupTreatment.Followup is G…

Comment: [ChIP-seq] DESeq2 on counts matrix from union set of called peaks by Luca • 0

I noticed the dual populations as well, when using csaw this is controlled for. Regarding the DE profile, given this disease condition we e…

Answer: Origin of the labels for the SingleCellMultiModal dataset by ATpoint ★ 4.8k

If you check the underlying code a bit you find that there is a file with data sources: ```r modes_file <- system.file("extdata", "metadat…

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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder

Comment: DESeq - help with pair wise comparisons

Answer: Is random access by row index possible for an indexed VCF file?

Answer: SingleR with multiple single cell references

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