Bioconductor SingleCellWorkflow

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SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData

2.5 years ago k1m ▴ 20

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SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment

2.5 years ago Romina • 0

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SingleCellWorkflow DifferentialExpression SingleCell SingleCellMultiModal MAST

2.8 years ago Nik Tuzov ▴ 90

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SingleCellSignalR SingleCellWorkflow SingleR

updated 16 months ago by Assa Yeroslaviz ★ 1.5k • written 3.9 years ago by FantasticAI ▴ 10

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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: Merging annotation with differential expression output

Answer: Explannation for ROAST results

Comment: Limma comparing gene expression between base line and one treatment

Answer: Is there any chance to solve "the model matrix is not full rank" in DESeq2?

clusterProfiler-GO enrichment Error

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