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scuttle
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Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
4 days ago
cathalgking
• 0
0
votes
1
reply
87
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 11 days ago by
alan.ocallaghan
▴ 120 • written 28 days ago by
cathalgking
• 0
2
votes
2
replies
479
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts
scran
librarySizeFactors
scuttle
scRNAseq
11 months ago
behr201
• 0
3
votes
3
replies
820
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
15 months ago
enricoferrero
▴ 650
4
votes
5
replies
1.1k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 2.1 years ago by
Aaron Lun
★ 28k • written 2.1 years ago by
enricoferrero
▴ 650
3
votes
4
replies
3.3k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
enricoferrero
▴ 650
6 results • Page
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Comment: Which input file is used for DGEList in EgdeR?
by
mohammedtoufiq91
▴ 10
Thank you @gordonsmyth My collaborator asked me to test this pipeline with `egdeR` package. We are interested at gene level analysis only…
Answer: Why in Bioconductor community people rarely upvote questions?
by
Gordon Smyth
47k
I think it is a good idea to start a discussion with correct information. Looking back through Bioconductor Support records, it is not at a…
Comment: How to identify top most variable genes from log2 normalized data?
by
Gordon Smyth
47k
Your code doesn't look right to me. I think you're using order() where sort() would be more appropriate. To order your cpm matrix by row v…
Comment: How to load fasta file with openPrimeR?
by
Santiago Edilberto
• 0
> library(openPrimeR) There are missing/non-functioning external tools. To use the full potential of openPrimeR, please mak…
Answer: Which input file is used for DGEList in EgdeR?
by
Gordon Smyth
47k
I use and recommend featureCounts. Despite all that has been written on this topic, I still think that direct gene counting is faster and m…
Votes
Answer: Which input file is used for DGEList in EgdeR?
Answer: Identifying DEGs using lfcshrink()
Answer: Is this DESeq2 interactions design correct?
Comment: STRINGdb string_db$map error
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
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