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rtracklayer browseGenome save file image UCSC

updated 6.0 years ago by maximilianh ▴ 10 • written 7.8 years ago by James Perkins ▴ 60

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vcf predict coding save file VariantAnnotation

updated 8.3 years ago by Thomas Sandmann ▴ 80 • written 8.3 years ago by anastasiya-terskih ▴ 10

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

I am reluctant 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

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