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catchSalmon edgeR

updated 10 months ago by Gordon Smyth 45k • written 10 months ago by Ina Hoeschele ▴ 620

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catchSalmon edgeR

20 months ago ATpoint ★ 1.3k

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Comment: LogFC: how do you determine the cutoff for differentially expressed genes? by OE • 0

Hi Aaron, I have been performing some Diffrential Methylation Analysis and found some logFC values really closer to 0 ( from - 0.07 to 0.1…

Comment: Macbook M1 install genefilter failed by matt.broerman • 0

This error is similar to this one: https://stackoverflow.com/questions/66817276/how-to-install-rcpparmadillo-on-apple-silicon-m1-macs So i…

Comment: miRNA differential expression analysis - treat as transcript level? by BG • 0

Hi, attached is the plot for the inferential variance (code according to the fishpond vignette). How does this look to you? The first plot …

Answer: miRNA differential expression analysis - treat as transcript level? by Michael Love 37k

If it's "ok" depends on the amount of inferential uncertainty. We have benchmarked typical gene-level methods and found that we don't gain …

Comment: RSEM - tximport; where is effective_length information used? Implications for sc by Michael Love 37k

@atpoint is correct -- it's not enough to say single-cell. In the tximport vignette we have a note about transcript length correction for 3…

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Teacher to Michael Love 37k