Showing : scater • reset
2
votes
1
reply
255
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by ★ 1.5k
3
votes
3
replies
456
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 7 weeks ago by ▴ 160 • written 7 weeks ago by • 0
3
votes
3
replies
417
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
1
vote
1
reply
266
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 3 months ago by ▴ 160 • written 3 months ago by ★ 1.5k
1
vote
7
replies
6.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 11 weeks ago by 16k • written 6 months ago by ▴ 10
0
votes
3
replies
1.1k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
6
replies
896
views
plotHeatmap annotation error
plotHeatmap scater
11 months ago Alina • 0
1
vote
0
replies
1.3k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
15 months ago cathalgking ▴ 10
0
votes
1
reply
683
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 15 months ago by ▴ 160 • written 16 months ago by ▴ 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
19 months ago Guandong Shang ▴ 40
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 21 months ago by ★ 28k • written 21 months ago by ▴ 40
3
votes
2
replies
1.7k
views
FeaturePlot in scater
scater OSCA
22 months ago Guandong Shang ▴ 40
5
votes
4
replies
1.7k
views
scater runUMAP
scater runUMAP
2.1 years ago jianhai.zhang • 0
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
2
votes
7
replies
1.7k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 2.2 years ago by ▴ 270 • written 2.2 years ago by ▴ 10
1
vote
2
replies
943
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.3 years ago • updated 2.2 years ago msn ▴ 10
0
votes
6
replies
2.9k
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 2.2 years ago by ▴ 160 • written 2.3 years ago by • 0
1
vote
2
replies
1.2k
views
More than 3 dimensions in runTSNE
dimensions scater runTSNE
2.5 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
2.6 years ago enricoferrero ▴ 660
2
votes
2
replies
1.3k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
2.9 years ago doliv071 • 0
2
votes
3
replies
1.3k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.3 years ago by ▴ 160 • written 3.3 years ago by • 0
3
votes
2
replies
2.3k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.3 years ago camerond • 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 660
2
votes
7
replies
2.6k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
votes
0
replies
784
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.5 years ago hamza_karakurt ▴ 50
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 ★ 28k • written 3.6 years ago by ▴ 60
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF scater
3.6 years ago lirongrossmann ▴ 40
0
votes
1
reply
1.1k
views
Change annotation colors plotHeatmap
scater plotHeatmap
3.7 years ago simone.avesani22 • 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ★ 4.1k
0
votes
1
reply
1.2k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
votes
4
replies
1.2k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 4.1 years ago by ★ 28k • written 4.2 years ago by ★ 2.0k
2
votes
4
replies
2.4k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.3 years ago by • 0 • written 4.2 years ago by • 0
0
votes
1
reply
1.0k
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 20
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
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 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.9 years ago Bogdan ▴ 670
0
votes
1
reply
840
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 350
8
votes
4
replies
2.3k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.2 years ago by • 0 • written 5.1 years ago by ▴ 10
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 50
7
votes
3
replies
3.3k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 10
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
50 results • Page 1 of 1
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Answer: Subsetting RNAseq data | voomaByGroup() by Gordon Smyth 50k
Judging from your MDS plot, cell types 1 and 2 look radically different, so it would make perfect sense to analyse them separately. There's…
Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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