Bioconductor Peaks

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472

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ATACSeq peaks ATAC ChIPpeakAnno

7 months ago Raghad • 0

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956

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Peaks MAC2 DiffBind

3.5 years ago Yuan Tian ▴ 290

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1.1k

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nucleosome peaks error Job

updated 5.1 years ago by James W. MacDonald 67k • written 5.1 years ago by anne.kannengiesser • 0

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3.0k

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diffbind chipseq counts peaks bedtools

updated 3.7 years ago by Rory Stark ★ 5.2k • written 6.7 years ago by Ni-Ar ▴ 10

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4.7k

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diffbind chipseq peaks dba is.na

6.7 years ago maria.kondili ▴ 10

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1.6k

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bioconductor annotation peaks

updated 7.1 years ago by Sean Davis 21k • written 7.1 years ago by schaud24 ▴ 10

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

Sorry, I had forgotten estimateGLMDisp() produces weights as well as NB dispersions. The weights from estimatGLMRobustDisp() were intended …

Answer: Mean variance curve troubleshoot filtering by Gordon Smyth 52k

You could use `filterByExpr()`, as recommended by Law et al (2018) and in the limma and edgeR case studies. However, the main problem wi…

Comment: How do I fix an odd voom plot in a combined dataset? by Gordon Smyth 52k

The fact that you have partial NA coefficients indicates that your merged dataset consists in good part of NAs for a very large number of g…

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…

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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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