3 months ago • updated 23 days ago
jamie.gearing
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updated 11 weeks ago by
SE
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written 9 months ago by
kieran.short
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3
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2
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updated 10 months ago by
Gordon Smyth
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agustin.gonvi
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jon.klonowski
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updated 12 months ago by
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14 months ago
mchakiachvili
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Kevin Blighe
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23 months ago • updated 21 months ago
mchakiachvili
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2.2 years ago
mchakiachvili
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tommaso.gastaldi
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lirongrossmann
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Kevin Blighe
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2.5 years ago
mchakiachvili
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updated 22 months ago by
Kevin Blighe
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written 2.6 years ago by
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2.7 years ago
Johannes Rainer
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updated 2.8 years ago by
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nina.hahn
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2.8 years ago
Assa Yeroslaviz
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815
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updated 2.8 years ago by
James W. MacDonald
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didemdkn
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296
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2.9 years ago
Astrid_Ensembl
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4
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4
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Ni-Ar
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mohsamir2016
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419
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11
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933
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3.1 years ago
dmgatti
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3.2 years ago
loicborcard01
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6
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Mike Smith
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swbarnes2
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written 3.3 years ago by
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3.6 years ago
Didi
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Johannes Rainer
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3.6 years ago
James Allen
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Mike Smith
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ktd2918
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wes
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Marc Saric
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Getting CDSCHROM values from ENSEMBL/SYMBOL keys using mapIds from TxDb.Hsapiens.UCSC.hg19.knownGene
updated 3.8 years ago by
James W. MacDonald
62k
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written 3.8 years ago by
kushshah
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Answer: struggling to create a heatmap
by
ATpoint
★
2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★
2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★
2.1k
You can take over some of the lines from `results()` to find them easily:
```r
suppressPackageStartupMessages(library(DESeq2))
set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
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