Biostar SNPs

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1.8k

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snps VCF

updated 9 months ago by Arafat • 0 • written 5.9 years ago by rkdonthu ▴ 10

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245

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hierClust R SNPs clustering

updated 10 months ago by James W. MacDonald 62k • written 10 months ago by sekhwal • 0

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431

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SNPs

3.9 years ago pltbiotech_tkarthi • 0

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816

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snps vcf venn diagram ggplot2

4.1 years ago mictadlo ▴ 10

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793

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bioconductor molecular biology snps

updated 4.2 years ago by James W. MacDonald 62k • written 4.2 years ago by jebreen20 • 0

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1.8k

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motifbreakR vcf snps motif analysis

updated 4.6 years ago by Valerie Obenchain ★ 6.7k • written 4.6 years ago by svlachavas ▴ 800

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1.0k

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variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc

updated 5.6 years ago by Valerie Obenchain ★ 6.7k • written 5.6 years ago by Lna • 0

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1.1k

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hsapiens snps indels

updated 7.2 years ago by Hervé Pagès 16k • written 7.2 years ago by kredens • 0

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1.1k

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Biostrings SNPs alignment

updated 7.5 years ago by Hervé Pagès 16k • written 7.6 years ago by ben.ward ▴ 30

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1.4k

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gviz ideogram snps

updated 8.0 years ago by florian.hahne@novartis.com ★ 1.6k • written 8.0 years ago by vnyirongo • 0

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1.6k

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overlap snps granges iranges

updated 8.3 years ago by Michael Lawrence 11k • 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

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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