Bioconductor DDS

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529

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DESeqDataSetFromMatrix dds DESeq2

updated 17 months ago by James W. MacDonald 68k • written 17 months ago by naomi.croft • 0

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671

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

updated 2.3 years ago by James W. MacDonald 68k • written 2.3 years ago by Enzo.Scifo • 0

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1.4k

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deseq2 cooks distance dds

updated 6.4 years ago by Michael Love 43k • written 6.4 years ago by ipso • 0

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1.3k

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deseq2 dds RPKM

updated 6.8 years ago by Michael Love 43k • written 6.8 years ago by harry.horsnell.17 • 0

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2.5k

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deseq2 rld pheatmap dds

updated 7.3 years ago by Michael Love 43k • written 9.4 years ago by rahel14350 ▴ 10

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5.7k

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deseq2 DDS

updated 7.4 years ago by Michael Love 43k • written 7.4 years ago by rrcutler ▴ 70

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5.2k

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Deseq2 dds confounders

updated 9.2 years ago by Michael Love 43k • written 9.2 years ago by colaneri ▴ 30

7 results • Page 1 of 1

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Answer: SingleR with multiple single cell references by Aaron Lun ★ 28k

> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…

Answer: Automatically install dependencies by ATpoint ★ 4.7k

The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…

Answer: To count or not to count multi-overlapping reads? by Gordon Smyth 52k

> How does it handle reads that map to a gene that is located in a region that also has another gene but on the alternate strand? Overlapp…

Comment: Weird p-values using DESeq2? by ATpoint ★ 4.7k

This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…

Answer: Weird p-values using DESeq2? by Wolfgang Huber ★ 13k

Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…

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A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo

Comment: Weird p-values using DESeq2?

Comment: Overcoming confounding in batch effect correction

Answer: Store Matrix in DataFrame Cell

Answer: enrichGOgradient color change

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Popular Question to maltethodberg ▴ 180