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scuttle
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 3 days ago by
ATpoint
★ 4.0k • written 3 days ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1.0k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 6 months ago by
ATpoint
★ 4.0k • written 6 months ago by
Abbi Edwards
• 0
1
vote
0
replies
1.2k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
13 months ago
cathalgking
▴ 10
0
votes
1
reply
600
views
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
views
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
views
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
8 results • Page
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Comment: miRTarRnaseq library
by
mercedeh.movassagh
▴ 10
Yes that is correct
Comment: What benchmark should I use for setting the EdgeR filterByExpr min.count paramet
by
Gordon Smyth
50k
It is the minimum group size rather than the total number of samples that is relevant. `min.prop` is more a biological parameter rather th…
Answer: Microarray Limma Model fitting and DEG
by
Gordon Smyth
50k
This dataset seems straightforward to analyse using the original MAS expression values on GEO. MAS expression values are known to be noisy …
Answer: Trimming a section of a scaffold from a genome
by
James W. MacDonald
65k
It's undoubtedly possible, but you don't provide enough information to go on. If I assume you are talking about an existing `BSgenome` pack…
Comment: DEG Filtering
by
Gordon Smyth
50k
I already know that you using CEL files because you need them to perform RMA normalization. Yes, you should follow the advice I have alread…
Votes
DESeq2 normalization vs VST vs rlog
Answer: DESeq2 "Contrast" option
Answer: error in ChAMP loading file
Circumvent creating .ff files in the working directory when using genotype.Illumina() function
Answer: Problem with maplot {affy} method when using rma {affy} method output as its inp
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