Bioconductor RNA-Seq

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deseq2 edgeR rna-seq

updated 1 day ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

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3.5k

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RNA-seq featureCounts ht-seq

written 3.7 years ago by ag1805x ▴ 80

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Spike-in RNASeqR DESeq2 Normalization rna-seq

updated 7 months ago by manuel.fernandez • 0 • written 2.0 years ago by cicely.day • 0

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2.2k

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isoformswitchanalyzeR rna-seq splice-variants

written 5.0 years ago by saddamhusain77 • 0

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1.5k

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GeneExpression GenomicFeatures RNA-Seq TPM

updated 7 months ago by Gordon Smyth 50k • written 7 months ago by gingergeiger22 • 0

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gage rna-seq pathwayanalysis

updated 11 months ago by Rob • 0 • written 3.5 years ago by microPhD • 0

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filtering RNA-Seq CPM edgeR filterByExpr

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

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894

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correlation pearsoncorrelation rna-seq differential gene expression

updated 4 months ago by ATpoint ★ 4.0k • written 6.0 years ago by saad_k6 • 0

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839

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BatchEffect lfcshrink RNA-seq DESeq2

8 months ago Eva ▴ 10

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831

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RNA-Seq sequencer library_size sequency_depth multiplexing offtopic

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

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691

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RNA-Seq normalization PCR_efficiency bias intrasample_comparison

updated 11 months ago by James W. MacDonald 65k • written 11 months ago by FedeXander • 0

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663

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RNA-seq DESeq2

6 months ago ar14g12 • 0

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660

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rna-seq salmon fishpond swish

updated 10 months ago by Michael Love 41k • written 10 months ago by samuelcjx • 0

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631

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DEXSeq RNA-seq DESeq2

updated 7 months ago by Alejandro Reyes ★ 1.9k • written 7 months ago by Alice • 0

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297

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RNA-Seq WGCNA Worms

4 months ago davca • 0

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258

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rna-seq edgeR

updated 4 days ago by Gordon Smyth 50k • written 11 days ago by Netanel • 0

16 results • Page 1 of 1

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Comment: DESeq filtering specific to contrasts by Michael Love 41k

It will likely not filter it out, but really the per-dataset details would affect the results.

Comment: DESeq filtering specific to contrasts by Carlin95 • 0

Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…

Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10

Thank you for your answer; However, I have some follow-up questions. Following up in In your [1-2-3 article][1], you say that > "... the…

Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0

Thank you very much for your reply! I will do so. Kind regards, Seyram

Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0

Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…

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Install/Switch between multiple versions of R, Rstudio, and Bioconductor

A: Docker container with bioconductor and devtools

Answer: OrgDb for maize

Comment: significant difference of p-values with dream() after updating VariancePartition

How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output

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