Bioconductor NA

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IRanges GRanges NA

updated 2.3 years ago by ATpoint ★ 4.6k • written 2.3 years ago by Timucin • 0

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pvalue NA R DESeq2

updated 3.1 years ago by ATpoint ★ 4.6k • written 3.1 years ago by Johan Largo • 0

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qCount QuasR NA

updated 4.4 years ago by Michael Stadler ▴ 350 • written 4.4 years ago by jabbar_campbell • 0

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limma mass spec na

updated 5.8 years ago by Gordon Smyth 52k • written 5.8 years ago by reubenmcgregor88 • 0

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methylkit normalizecoverage NA

updated 6.2 years ago by altuna akalin ▴ 20 • written 6.2 years ago by GFM ▴ 20

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deseq2 coldata NA

updated 4 months ago by Michael Love 43k • written 6.4 years ago by t.kuilman ▴ 170

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edger dgelist NA egsea

updated 6.9 years ago by Gordon Smyth 52k • written 6.9 years ago by belmore • 0

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rtracklayer NA

8.3 years ago Dario Strbenac ★ 1.5k

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reportingtools deseq2 NA pvalue

updated 8.5 years ago by Michael Love 43k • written 8.5 years ago by NMostajo ▴ 10

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deseq2 NA cooksCutoff

updated 8.8 years ago by Michael Love 43k • written 8.8 years ago by colaneri ▴ 30

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gwastools lrr baf NA

updated 9.1 years ago by Stephanie M. Gogarten ▴ 890 • written 9.1 years ago by Vinicius Henrique da Silva ▴ 40

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rtracklayer NA BED getseq

9.1 years ago Dimitris Polychronopoulos ▴ 80

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graphics confidence interval NA

updated 9.2 years ago by James W. MacDonald 67k • written 9.3 years ago by Vinicius Henrique da Silva ▴ 40

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Gviz Plot NA graph Job

updated 9.4 years ago by James W. MacDonald 67k • written 9.4 years ago by Vinicius Henrique da Silva ▴ 40

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parody r NA

9.8 years ago upendrakumar.devisetty • 0

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snpStats BioConductor LD Linkage Disequilibrium NA

9.9 years ago remi.tournebize ▴ 10

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deseq2 cook NA

updated 10.2 years ago by Michael Love 43k • written 10.2 years ago by skiaphrene ▴ 10

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EdgeR rnaseq NA

updated 10.3 years ago by Aaron Lun ★ 28k • written 10.3 years ago by elliott77 • 0

18 results • Page 1 of 1

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Replies

Comment: How do I fix an odd voom plot in a combined dataset? by 1sunmic2 • 0

Thanks for responding! I did change the code slightly: dge1 <- DGEList(counts = combined_data_counts) keep <- rowSums(cpm(dge1)…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Andre • 0

The estimateGLMRobustDisp() function seems to have an effect on glmQLFit(), even in edgeR 4 (4.4.1). If I use estimateGLMRobustDisp(), like…

Comment: Incorporating Salmon offset matrix into Wilcoxon DEG analysis by Gordon Smyth 52k

Here, estimateGLMRobustDisp() was used just to get the diagnostic BCV plot by plotBCV(y). The robust NB dispersions were not used for the D…

Answer: Please, I desperately need help with DESeq2. Three groups of repeated measures w by Michael Love 43k

I have to reserve my time on the support site for software related questions. I recommend working with a local statistician or someone fami…

Answer: Is it possible to work with DESeq2 where data is not properly matched for sex a by Michael Love 43k

I would probably just do the M vs M analysis. You could instead include a term for sex and have a model with all 45 samples, but the M vs M…

Votes

Answer: How do I fix an odd voom plot in a combined dataset?

Comment: How do I fix an odd voom plot in a combined dataset?

C: How does edgeR cpm function calculate log(CPM) values?

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