Biostar GenomicFiles

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628

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GenomicFiles ShortRead Rsamtools

23 months ago robmaz77 ▴ 20

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802

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GenomicFiles BiocParallel

updated 5.6 years ago by shepherl 3.4k • written 5.7 years ago by m.van_iterson ▴ 20

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979

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rsamtools genomicalignments genomicfiles

updated 6.6 years ago by Hervé Pagès 16k • written 6.6 years ago by jfiksel ▴ 30

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409

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GenomicFiles

updated 3.8 years ago by Martin Morgan 25k • written 3.8 years ago by Qiang ▴ 70

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2.1k

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rsamtools genomicalignments genomicfiles

updated 7.5 years ago by Martin Morgan 25k • written 7.5 years ago by Welliton de Souza ▴ 70

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835

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genomicfiles reduceByRange

updated 5.4 years ago by Valerie Obenchain ★ 6.7k • written 5.4 years ago by maltethodberg ▴ 140

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644

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genomicfiles

updated 5.1 years ago by Martin Morgan 25k • written 5.1 years ago by Qiang ▴ 70

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995

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genomicfiles rsamtools

updated 6.6 years ago by Martin Morgan 25k • written 6.6 years ago by victoriaccorey ▴ 10

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277

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GenomicInteractions Basic4Cseq DNASeq GenomicFiles

19 months ago koushik • 0

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774

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GO Biostrings rtracklayer GenomicRanges BiocParallel GenomicFiles

8.4 years ago Dan Tenenbaum ★ 8.2k

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Answer: struggling to create a heatmap by ATpoint ★ 2.1k

I am recuctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…

Answer: collapseReplicates error after tximeta by Michael Love 39k

The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…

Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it by ATpoint ★ 2.1k

That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…

Answer: Which genes are outliers in DESeq2? by ATpoint ★ 2.1k

You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…

Answer: Which genes are outliers in DESeq2? by Michael Love 39k

Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…

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Significant reporter activity with mpralm function

Answer: I cannot install annotables package in Rstudio (macOS)

Answer: log2 of normalized counts for further analyzes

Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it

Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used

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