Bioconductor Rna-seq

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deseq2 edgeR rna-seq

updated 4 weeks ago by Elizabeth • 0 • written 8.9 years ago by gthm ▴ 30

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filtering RNA-Seq CPM edgeR filterByExpr

updated 12 months ago by Gordon Smyth 50k • written 12 months ago by mohammedtoufiq91 ▴ 10

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896

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BatchEffect lfcshrink RNA-seq DESeq2

9 months ago Eva ▴ 10

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371

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rna-seq edgeR

updated 4 weeks ago by Gordon Smyth 50k • written 6 weeks ago by Netanel • 0

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184

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DESeq2 PCAplot RNA-Seq DesignModel

updated 18 hours ago by Michael Love 42k • written 3 days ago by shaunpeterson • 0

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263

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RNA-seq DESeq2

updated 16 days ago by ATpoint ★ 4.1k • written 17 days ago by Reza • 0

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GeneExpression GenomicFeatures RNA-Seq TPM

updated 8 months ago by Gordon Smyth 50k • written 8 months ago by gingergeiger22 • 0

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288

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rna-seq duplicateCorrelation limma voom

12 days ago • updated 11 days ago Dylan.Sheerin • 0

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327

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RNA-Seq WGCNA Worms

6 months ago • updated 5 months ago davca • 0

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2.3k

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 8 months ago by manuel.fernandez • 0 • written 2.1 years ago by cicely.day • 0

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712

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rna-seq salmon fishpond swish

updated 11 months ago by Michael Love 42k • written 11 months ago by samuelcjx • 0

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RNA-seq featureCounts ht-seq

written 3.8 years ago by ag1805x ▴ 80

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737

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RNA-seq DESeq2

7 months ago ar14g12 • 0

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921

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correlation pearsoncorrelation rna-seq differential gene expression

updated 5 months ago by ATpoint ★ 4.1k • written 6.1 years ago by saad_k6 • 0

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isoformswitchanalyzeR rna-seq splice-variants

written 5.1 years ago by saddamhusain77 • 0

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698

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DEXSeq RNA-seq DESeq2

updated 8 months ago by Alejandro Reyes ★ 1.9k • written 8 months ago by Alice • 0

16 results • Page 1 of 1

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Comment: Ensembl plants at annotationHub? by Johannes Rainer ★ 2.0k

You can get the `EnsDb` EnsDb.Taestivum.v112.sqlite (for Ensembl 112/ ensemblgenomes 59) [here](https://www.dropbox.com/sh/msic0luivbldmb7/…

Comment: Errors in chromosome annotation-biomaRt by blackwidowzzz • 0

I recommend using a different dataset specific to your rat genome assembly version 8. You can search for available datasets within Ensembl …

Answer: Errors in chromosome annotation-biomaRt by James W. MacDonald 66k

If you are just using HGNC symbols for the lookup, and you are trying to get NCBI IDs, then I wouldn't use `biomaRt` because it's based on …

Comment: Help with ENmix readidat by James W. MacDonald 66k

Please don't add to posts from two years ago. Instead make a new post. Also, please read the help page for `readidat`. The only reason to …

Comment: LRT, more than two conditions and pairwise comparisons by James W. MacDonald 66k

In that case, probably easiest to subset to the groups being compared.

Votes

Answer: Error retrieving ensembl gene id using biomaRt...

Comment: LRT, more than two conditions and pairwise comparisons

Answer: Control group between 2 batches have different expression in RNAseq data

Answer: How to remove batch effect to combine RNAseq data from 2 different experiments?

Comment: DESeq2- Mysterious interaction suppresses DEGs

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