Bioconductor RNA-Seq

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rna-seq edgeR

updated 5 days ago by Gordon Smyth 50k • written 18 days ago by Netanel • 0

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deseq2 edgeR rna-seq

updated 7 days ago by Elizabeth • 0 • written 8.8 years ago by gthm ▴ 30

2 results • Page 1 of 1

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Answer: ATACseq merge peaks by ATpoint ★ 4.0k

That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10

Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…

Comment: Deseq2. decontXcounts not integers. Useful alternative? by ATpoint ★ 4.0k

I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…

Answer: Improving the design matrices vignette in RNAseq123 by Gordon Smyth 50k

Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…

Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by winwater0928 • 0

Thank you for your comment! I'll review my code from top to bottom.

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biomaRt error: database disk image is malformed

Comment: biomaRt : No lock file for BiocFileCache

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