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Profiling bioconductor packages in a straightforward fashion
HPC
profiling
performance
3.2 years ago
Jack
• 0
0
votes
5
replies
1.7k
views
How to plot benchmark result of R/ Bioconductor package (getting curve or line graph)?
r
benchmark
performance
ggplot2
8.0 years ago
Jurat Shahidin
▴ 80
2
votes
2
replies
1.1k
views
Any way to speed up splitting relatively big GRanges objects by given threshold ?
r
granges
split
performance
updated 8.2 years ago by
Michael Lawrence
★ 11k • written 8.2 years ago by
Jurat Shahidin
▴ 80
1
vote
8
replies
2.7k
views
most efficient way to read adjacency matrix to make networkd3 graph
r
iterators
performance
updated 8.5 years ago by
phil.chapman
▴ 150 • written 8.5 years ago by
chrisclarkson100
▴ 50
1
vote
2
replies
1.5k
views
DESeq2 performance information for counts tables with very large rows number
deseq2
performance
8.8 years ago • updated 8.7 years ago
atisou
• 0
5 results • Page
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Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
James W. MacDonald
67k
How you analyze your data is up to you. But do note that Subset * Conditions implies that you want to find genes that respond to stimulus d…
Comment: MBDseq analysis using qsea package
by
kf
• 0
Hi Matthias, Happy new year! I wondered if it is possible to retrieve normalized value from each samples? makeTable seems only return beta…
Comment: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
Quang
• 0
Hi, James. I forgot to mention, but yes, I did run `DESeq2::DESeq()`. So, I ran `DESeq2::DESeqDataSetFromHTSeqCount`, then `DESeq2::DESeq()…
Answer: Why did PCA plots look exactly the same after adjusting for batch covariate in D
by
ATpoint
★ 4.6k
It's an FAQ in the vignette: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#why-after-vst-are-there-s…
Comment: Deseq2, enrichGO and ensembl ID
by
James W. MacDonald
67k
I am not sure I understand. You say that a unique Ensembl ID maps to multiple gene symbols. That doesn't mean you have two genes (it's just…
Votes
A: Trajectory analysis for single cell sequencing
Answer: Annotation with org.Hs.eg.db Genome Build 38
Answer: Annotation with org.Hs.eg.db Genome Build 38
Answer: Considerations behind the choice of RNAseq Differential Expression Analysis Tool
A: goana limma- extract list of DE genes and genes in the enriched GO terms?
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