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biocparallel
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Reproducibility issue with scran together with lapply and BiocParallel
scran
BiocParallel
bluster
11 days ago • updated 10 days ago
ATpoint
★ 4.1k
3
votes
3
replies
201
views
Reading huge bismark coverage files using bbseq::read.bismark
HDF5Array
BiocGenerics
BiocParallel
Biobase
22 days ago • updated 17 days ago
jacques.imbert
• 0
0
votes
3
replies
441
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel
scran
updated 3 months ago by
ATpoint
★ 4.1k • written 3 months ago by
qwang178
• 0
1
vote
4
replies
602
views
BiocParallel serialization errors on Windows
variancePartition
BiocParallel
4 months ago
hayleyw
• 0
0
votes
2
replies
1.2k
views
Error: BiocParallel errors
xcms
msdata
BiocParallel
8 months ago
mavamay
• 0
1
vote
11
replies
1.5k
views
BiocParallel 1.33.12 binary has incorrect library linkage on macOS x86
BiocParallel
updated 12 months ago by
Martin Morgan
25k • written 12 months ago by
Michael Steinbaugh
▴ 90
6 results • Page
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Comment: Too many significant genes when integrating gtex and tcga
by
ATpoint
★ 4.1k
These two datasets are from completely different experiments / batches. It is utterly meaningless to compare them. I would suggest comparat…
Answer: fgsea significant result
by
ATpoint
★ 4.1k
Set a fixed seed before running this. Note that a FDR of 0.25 in fgsea is wildly and overly lenient. See https://support.bioconductor.o…
Answer: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
Hi Michael, I think there is something wrong with the generation of nullranges. I was working with small RNA and methylation overlaps. …
Answer: Once again a "Model matrix not full rank"
by
swbarnes2
★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results?
by
Gordon Smyth
50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Votes
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
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