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scuttle
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 24 days ago by
ATpoint
★ 4.0k • written 24 days ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1.1k
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
1.3k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
14 months ago
cathalgking
▴ 10
0
votes
1
reply
630
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 14 months ago by
alan.ocallaghan
▴ 160 • written 15 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
2.2 years ago • updated 2.1 years ago
behr201
• 0
3
votes
3
replies
1.6k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.5 years ago
enricoferrero
▴ 660
4
votes
5
replies
2.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
enricoferrero
▴ 660
5
votes
4
replies
6.0k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
enricoferrero
▴ 660
8 results • Page
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Answer: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
by
Michael Love
41k
Starting from the very top, do you understand the error? You need to provide sample info that matches 1-to-1 the columns of the counts matr…
Answer: covariate with negative and positive values
by
Michael Love
41k
Not a problem. However, if the values are very large (eg 1e6) or very small (eg 1e-6), it's a good idea to center and scale the variable…
Comment: FilterByExpr low counts with small sample size
by
Jonathan
▴ 10
Usually I run `voomLmFit`, although in order to create the mean-variance trend plots for this particular post, I ran `voom`; I've checked -…
Comment: Error in champ.load(): The following specified files do not exist
by
Sherin
• 0
it worked! thank you so much!!
Comment: Multi factor design edgeR/Deseq2
by
Elizabeth
• 0
Sorry I realise this thread is ancient, but I'm wondering why it's ok to remove the last column from the design matrix? Also, why this desi…
Votes
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
Using GRanges and IRanges to simply get all chromosome data
A: Using GRanges and IRanges to simply get all chromosome data
Comment: Reading huge bismark coverage files using bbseq::read.bismark
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