Biostar Refseq

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606

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refseq Bioconductor conversion

2.2 years ago heiko_kin ▴ 50

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261

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RefSeq Chromosome Mutalyzer

2.8 years ago heiko_kin ▴ 50

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940

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tximport Gene IDs txdb RefSeq Salmon

updated 3.0 years ago by Michael Love 39k • written 3.0 years ago by holmkn • 0

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2.1k

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edgeR ENEMBL RefSeq

updated 3.9 years ago by Gordon Smyth 47k • written 3.9 years ago by mzillur • 0

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2.1k

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genomicfeatures maketxdbfromucsc refseq

updated 6.5 years ago by Hervé Pagès 16k • written 6.5 years ago by Sebastien Vigneau ▴ 10

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2.6k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 7.0 years ago by Hervé Pagès 16k • written 7.0 years ago by gokcen.eraslan ▴ 10

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1.8k

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promoter granges refseq ucsc organismdb

updated 7.2 years ago by Robert Castelo ★ 3.0k • written 7.2 years ago by efoss ▴ 10

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3.1k

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refseq annotationhub

updated 7.4 years ago by Martin Morgan 25k • written 7.4 years ago by dalloliogm ▴ 40

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1.2k

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customprodb dbsnp refseq varianttools

updated 7.6 years ago by xiaojing.wang ▴ 50 • written 7.6 years ago by kristenbeck527 • 0

9 results • Page 1 of 1

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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…

Votes

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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