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11
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14 hours ago Gilles • 0
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1
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20
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branchpointer: trouble to read gtf
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1 day ago Franck • 0
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1 day ago xiaoleiusc • 0
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2 days ago Koki ▴ 10
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6 days ago Laura • 0
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92
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MSstatsPTM - Maxquant - MaxQtoMSstatsPTMFormat - Phosphorylation
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updated 12 days ago by ★ 5.1k • written 12 days ago by • 0
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15 days ago FWNL15 • 0
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16 days ago Francois Marchildon ▴ 20
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updated 18 days ago by 3.4k • written 20 days ago by • 0
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20 days ago Charles • 0
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20 days ago catherine.li • 0
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21 days ago Gian ▴ 30
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updated 21 days ago by 15k • written 21 days ago by • 0
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Enlarge arrows representing introns in Gene Region Track Gviz
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21 days ago rbenel ▴ 20
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23 days ago cer.chloe ▴ 20
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23 days ago Guandong Shang ▴ 20
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25 days ago xuyao15927402897 • 0
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featureCounts: unable to find chromosome in SAM header
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updated 23 days ago by • 0 • written 27 days ago by • 0
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27 days ago rajya82 • 0
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29 days ago mb1996 • 0
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4 weeks ago • updated 18 days ago Jinyue • 0
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4 weeks ago Davide • 0
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4 weeks ago Dmitri • 0
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Construct a phyloseq object directly from the dada2 outputs
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4 weeks ago Manijeh • 0
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Replies
Comment: Per gene Covariates by Michael Love 34k
If you have per gene and per sample corrections, you can use normalization factors (see DESeq2 paper and vignette first on this topic). Fo…
Comment: deseq2 machine sizing best practices for very large data set by Michael Love 34k
I recommend and use limma-voom for large bulk datasets often, it is much faster than GLM-based methods.
Comment: branchpointer: trouble to read gtf by b.signal • 0
Hi Frank, Your example gtf is missing a gene_id. In the old code we also required a transcript_type/transcript_biotype, and a gene_type/g…
Comment: deseq2 machine sizing best practices for very large data set by ATpoint ▴ 840
https://support.bioconductor.org/p/73399/#73400
Comment: Per gene Covariates by Paola • 0
Hi Michael, I have a similar problem where we want to run a LRT analysis on RNA-Seq to find differences across 4 groups and correcting for…
Votes
Answer: Format roxgen comment (alternative to formatR)
Format roxgen comment (alternative to formatR)
Answer: Format roxgen comment (alternative to formatR)
How does DESeq2 handle zero counts in one condition?
The calculation of regularized logarithm
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