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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 25 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
views
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
1.7k
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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Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
ATpoint
★ 4.0k
As expected normalization is **way** off, meaning in simple terms that the cloud is too high. The deep-blue area should be along y=0. Try t…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
Thank you for your suggestions! Here is the MA plot: ![enter image description here][1] I tried several normalization methods with DiffBi…
Answer: OrgDb for maize
by
Guido Hooiveld
★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question
by
Garrett
• 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing
by
sropri
• 0
Thank you!
Votes
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
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