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scran SingleCellExperiment scuttle scater

updated 6 months ago by Aaron Lun ★ 27k • written 6 months ago by enricoferrero ▴ 570

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scran scater scuttle

updated 12 months ago by Aaron Lun ★ 27k • written 12 months ago by enricoferrero ▴ 570

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Answer: tximeta countsFromAbundance for downstream analysis by Michael Love 33k

The counts will not be closely correlated to the TPM across genes, because the gene length is included in the gene count but not in the TPM…

Answer: DESeq2 - understanding intercept and contrasts by Michael Love 33k

For questions on setting up the statistical design and contrasts, I recommend to consult with a local statistician or someone familiar with…

Answer: Interaction terms and selection of coef in normal and shrunk results by Michael Love 33k

Please see the diagram in the vignette on interactions, but for further questions on setting up the design, I recommend to consult with a l…

Answer: about baseMean in DEseq2 by Michael Love 33k

More information about the columns is here: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#access-…

Answer: DESeq2, what to do when controls are 7 times more abundant than treatments by Michael Love 33k

I generally recommend your option 2 here: filtering out genes unless they are minimally expressed in the lowly sequenced condition. This is…

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A: plotPCA - how to add labels to a PCA plot

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Scholar to Michael Lawrence 11k