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DESeq2 Transcriptomics tximport deseq txi

updated 2.2 years ago by Dario Strbenac ★ 1.6k • written 2.2 years ago by Hicham ▴ 10

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TxDb.Sscrofa.UCSC.susScr11.refGene TxDb txi

updated 2.4 years ago by James W. MacDonald 68k • written 2.4 years ago by Luke • 0

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tx2gene txi error

updated 5.9 years ago by James W. MacDonald 68k • written 5.9 years ago by eliztran • 0

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Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20

I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…

Answer: Error in cnetplot by Guido Hooiveld ★ 4.1k

Unfortunately you did not show how you generated your input data (the object `enrichment`), nor did you show the output from `sessionInfo()…

Answer: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

I think this is because Ensembl can assign different Gene IDs to "the same gene" if it is found both on a standard chromosome and a scaffol…

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Answer: Explannation for ROAST results

clusterProfiler-GO enrichment Error

A: Machine learning in R book

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