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scuttle
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 4 days ago by
ATpoint
★ 4.0k • written 4 days ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1.0k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 7 months ago by
ATpoint
★ 4.0k • written 7 months ago by
Abbi Edwards
• 0
1
vote
0
replies
1.2k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
14 months ago
cathalgking
▴ 10
0
votes
1
reply
603
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cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 14 months ago by
alan.ocallaghan
▴ 150 • written 14 months ago by
cathalgking
▴ 10
2
votes
2
replies
1.2k
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
2.1 years ago
behr201
• 0
3
votes
3
replies
1.6k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.4 years ago
enricoferrero
▴ 660
4
votes
5
replies
2.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
enricoferrero
▴ 660
5
votes
4
replies
5.9k
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scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
enricoferrero
▴ 660
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Comment: limma models out of memory issue on Slurm HPC
by
SamGG
▴ 330
> Alternatively you could run each linear model fit (var1 to var6) in a separate batch run, and again that would presumably work. I think …
Comment: fgsea fork
by
shepherl
3.8k
For What its worth BiocManager should also be able to install the github remotes `BiocManager::install("ctlab/fgsea")`
Comment: fgsea fork
by
alserg
▴ 240
I'm also not sure what you mean by fork, but you also can install the latest version of fgsea directly from GitHub with `devtools::install_…
Comment: limma models out of memory issue on Slurm HPC
by
Jitendra
▴ 10
thanks Gordon, but our methylation epic array input file is quite big and we can't read it in R by just using laptop memory so we need to …
Comment: Doing comparison of RNA-seq data using EdgeR
by
Michael Love
41k
Just to clarify, when I originally posted the title and tags had listed "DESeq2" and then the post was changed after my answer was added. …
Votes
transcript name mapping between human and mouse
transcript name mapping between human and mouse
A: Error object and replacement value dimnames differ, when changing column names o
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
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