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single GenomeInfoDb

updated 2.6 years ago by Yichao • 0 • written 3.6 years ago by Francesco Monticolo • 0

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scran single cell

updated 3.7 years ago by Aaron Lun ★ 29k • written 3.7 years ago by hemantcnaik • 0

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edgeR single scRNAseq

4.1 years ago • updated 3.9 years ago mbenegas ▴ 10

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scater single SingleCellExperiment

updated 3.7 years ago by Aaron Lun ★ 29k • written 4.8 years ago by p.joshi ▴ 40

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1.5k

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limma custom diagnostic plots single

updated 9.9 years ago by Gordon Smyth 52k • written 9.9 years ago by dario.veneziano • 0

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limma single genepix normalization technical

9.9 years ago dario.veneziano • 0

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Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long by mohammedtoufiq91 ▴ 10

@gordonsmyth thanks. The above plots are obtained by edgeR steps provided below: ``` # Load required libraries library(edgeR) library(read…

Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long by Gordon Smyth 52k

You should compute divided counts before estimating edgeR dispersions. These plots look like they are using raw counts. You could also try…

Comment: emptyDrops new default alpha = Inf giving far fewer non-empty droplets than unde by Peter Hickey ▴ 760

Thanks, Aaron. The PR returns a better looking knee-point than the current default on my data (knee = 2363). ![knee-point from 124][1] …

Answer: The default value of 'abundanceCol' by James W. MacDonald 68k

The default is dependent on the input. Mostly it's TPM, but for e.g., StringTie it's FPKM. You can always see the function body by typing t…

Comment: Transcript expression analysis in edgeR from gtf file obtained from merging long by mohammedtoufiq91 ▴ 10

@gordonsmyth thank you very much for the feedback. I will try to seek guidance from the author's of those packages as well. Anyways, this i…

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Answer: Transcript expression analysis in edgeR from gtf file obtained from merging long

Answer: Difference between logFC in limma-voom and weighted limma-voom

Answer: heatmap with batch effect

Answer: Limpa Pipeline Order

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