Bioconductor DDS

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2.3k

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deseq2 rld pheatmap dds

updated 6.5 years ago by Michael Love 42k • written 8.7 years ago by rahel14350 ▴ 10

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4.8k

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Deseq2 dds confounders

updated 8.4 years ago by Michael Love 42k • written 8.4 years ago by colaneri ▴ 30

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5.0k

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deseq2 DDS

updated 6.7 years ago by Michael Love 42k • written 6.7 years ago by rrcutler ▴ 70

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1.0k

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deseq2 dds RPKM

updated 6.1 years ago by Michael Love 42k • written 6.1 years ago by harry.horsnell.17 • 0

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1.2k

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deseq2 cooks distance dds

updated 5.7 years ago by Michael Love 42k • written 5.7 years ago by ipso • 0

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484

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Celegans DESeq2 dds Errorinseq_len(length(idx)-1)

updated 18 months ago by James W. MacDonald 66k • written 18 months ago by Enzo.Scifo • 0

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362

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DESeqDataSetFromMatrix dds DESeq2

updated 8 months ago by James W. MacDonald 66k • written 8 months ago by naomi.croft • 0

7 results • Page 1 of 1

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Comment: How to add Ensembl ids after Pseudobulk analysis by DESeq2 by BioinfGuru ▴ 30

I would use biomaRt. This is what happens when annotation occurs to early. If possible I would run the DEG analysis on the original output…

Comment: Volcano plot of scRNA-seq data not "centered" by ATpoint ★ 4.2k

My comment was generic. If your experiment causes drastic shifts then the situation might be different. The advise is the same: Try to use …

Comment: conumee with Infinium MethylationEPIC v2.0 by Maximus • 0

Hi Sole, If there is a combined mixture of MSet of 450K, EPIC and EPICv2, how should I create an annotation object? I tried to create anno…

Comment: Volcano plot of scRNA-seq data not "centered" by tjl • 0

Thank you both. The code is below, simplified a bit for simplicity. ATpoint, your suggestion re: the top 20% of genes by baseMean makes me …

Comment: Cannot install oligo on Fedora by James W. MacDonald 66k

Wait a minute. The `oligo` package is *supposed to* be using `zlibbioc`, but apparently it is not. I get the same thing as you do, where it…

Votes

A: Analyzing data without replicates using DiffBind

DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Gene symbol

DESeq2 swap ensembl gene id rownames with gene symbol column

A: DeSeq2 results converting ENSG IDs to Gene Symbols, more than one ENSG ID per Ge

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Popular Question to Robert Castelo ★ 3.3k