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Scater
•
reset
0
votes
4
replies
148
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
3 days ago • updated 2 days ago
vohara4
• 0
3
votes
3
replies
565
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 11 weeks ago by
alan.ocallaghan
▴ 160 • written 11 weeks ago by
Najla Abassi
• 0
2
votes
1
reply
299
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 11 weeks ago by
ATpoint
★ 4.2k • written 11 weeks ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
509
views
plotUMAP Gene Set Faceted
scater
updated 4 months ago by
alan.ocallaghan
▴ 160 • written 4 months ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
309
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 4 months ago by
alan.ocallaghan
▴ 160 • written 4 months ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
7.1k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 3 months ago by
Hervé Pagès
16k • written 7 months ago by
inzirio
▴ 10
0
votes
3
replies
1.2k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 9 months ago by
ATpoint
★ 4.2k • written 9 months ago by
Abbi Edwards
• 0
0
votes
6
replies
928
views
plotHeatmap annotation error
plotHeatmap
scater
12 months ago
Alina
• 0
1
vote
0
replies
1.4k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
16 months ago
cathalgking
▴ 10
0
votes
1
reply
718
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 16 months ago by
alan.ocallaghan
▴ 160 • written 17 months ago by
cathalgking
▴ 10
1
vote
2
replies
1.2k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
20 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.1k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 22 months ago by
Aaron Lun
★ 28k • written 22 months ago by
Guandong Shang
▴ 40
3
votes
2
replies
1.8k
views
FeaturePlot in scater
scater
OSCA
23 months ago
Guandong Shang
▴ 40
5
votes
4
replies
1.7k
views
scater runUMAP
scater
runUMAP
2.2 years ago
jianhai.zhang
• 0
2
votes
1
reply
1.2k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 2.2 years ago by
Basti
▴ 780 • written 2.2 years ago by
Lucky
• 0
0
votes
6
replies
3.0k
views
runPCA error / Error in runSVD(x, k = rank, nu = ifelse(get.pcs, rank, 0), nv = ifelse(get.rotation, : argument "rank" is missing, with no default
scater
updated 2.3 years ago by
alan.ocallaghan
▴ 160 • written 2.4 years ago by
tinyimp80
• 0
2
votes
7
replies
1.8k
views
calculateTSNE with large dataset
runTSNE
calculateTSNE
scater
updated 2.3 years ago by
mikhael.manurung
▴ 280 • written 2.3 years ago by
alaihd
▴ 10
1
vote
2
replies
971
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.3 years ago
msn
▴ 10
1
vote
2
replies
1.2k
views
More than 3 dimensions in runTSNE
dimensions
scater
runTSNE
2.6 years ago
jianhai.zhang
• 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.6 years ago
enricoferrero
▴ 660
2
votes
3
replies
1.2k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.7 years ago
enricoferrero
▴ 660
2
votes
2
replies
1.4k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
3.0 years ago
doliv071
• 0
2
votes
3
replies
1.4k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment
scater
updated 3.4 years ago by
alan.ocallaghan
▴ 160 • written 3.4 years ago by
rogerbear
• 0
3
votes
2
replies
2.3k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
3.4 years ago • updated 3.3 years ago
camerond
• 0
4
votes
5
replies
2.4k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
enricoferrero
▴ 660
2
votes
7
replies
2.7k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 2.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
p.joshi
▴ 40
0
votes
0
replies
798
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
3.6 years ago
hamza_karakurt
▴ 60
3
votes
3
replies
2.4k
views
What lengths are used to calculate TPM in "scater" package
scater
calculateTPM
RNAseq
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Matan G.
▴ 60
5
votes
5
replies
1.8k
views
Running NMF for single cell
NMF
scater
3.7 years ago
lirongrossmann
▴ 50
0
votes
1
reply
1.1k
views
Change annotation colors plotHeatmap
scater
plotHeatmap
3.8 years ago
simone.avesani22
• 0
5
votes
4
replies
6.2k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
enricoferrero
▴ 660
3
votes
1
reply
1.2k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
ATpoint
★ 4.2k
0
votes
1
reply
1.3k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment
sce
scater
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
bharris
• 0
0
votes
4
replies
1.2k
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Jenny Drnevich
★ 2.0k
2
votes
4
replies
2.4k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 3.4 years ago by
1498554536
• 0 • written 4.2 years ago by
Linda
• 0
0
votes
1
reply
1.0k
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
santos22903
• 0
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
moldach
▴ 20
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
hamza_karakurt
▴ 60
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Bogdan
▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
5.0 years ago
Bogdan
▴ 670
0
votes
1
reply
859
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
5.0 years ago
hamza_karakurt
▴ 60
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
kevin.rue
▴ 350
2
votes
4
replies
3.7k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 2.2 years ago by
Dayme
• 0 • written 5.2 years ago by
kushshah
▴ 10
8
votes
4
replies
2.4k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 60
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
kushshah
▴ 10
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.2 years ago by
Vladimir Kiselev
▴ 150 • written 5.2 years ago by
hamza_karakurt
▴ 60
7
votes
3
replies
3.3k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
kushshah
▴ 10
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Comment: gds in GEOmetadb 2023-06-26 version is empty
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Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
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You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
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