Showing : scater • reset
0
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4
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1.0k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
14 months ago vohara4 • 0
3
votes
3
replies
2.2k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 17 months ago by ▴ 160 • written 17 months ago by • 0
2
votes
1
reply
880
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 17 months ago by ★ 4.9k • written 17 months ago by ★ 1.6k
3
votes
3
replies
2.1k
views
plotUMAP Gene Set Faceted
scater
updated 19 months ago by ▴ 160 • written 19 months ago by ★ 1.6k
1
vote
1
reply
895
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 19 months ago by ▴ 160 • written 19 months ago by ★ 1.6k
1
vote
7
replies
9.8k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 18 months ago by 16k • written 21 months ago by ▴ 10
0
votes
3
replies
1.9k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 2.0 years ago by ★ 4.9k • written 2.0 years ago by • 0
0
votes
6
replies
1.5k
views
plotHeatmap annotation error
plotHeatmap scater
2.2 years ago Alina • 0
1
vote
0
replies
2.7k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.6 years ago cathalgking ▴ 10
0
votes
1
reply
1.3k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 2.6 years ago by ▴ 160 • written 2.6 years ago by ▴ 10
1
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2
replies
1.9k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.9 years ago Guandong Shang ▴ 40
0
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4
replies
2.9k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 3.1 years ago by ★ 29k • written 3.1 years ago by ▴ 40
3
votes
2
replies
2.7k
views
FeaturePlot in scater
scater OSCA
3.2 years ago Guandong Shang ▴ 40
5
votes
4
replies
2.6k
views
scater runUMAP
scater runUMAP
3.4 years ago jianhai.zhang • 0
2
votes
1
reply
1.8k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
0
votes
6
replies
4.1k
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 3.5 years ago by ▴ 160 • written 3.6 years ago by • 0
2
votes
7
replies
2.5k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 3.5 years ago by ▴ 280 • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.4k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.5 years ago msn ▴ 10
1
vote
2
replies
1.6k
views
More than 3 dimensions in runTSNE
dimensions scater runTSNE
3.8 years ago jianhai.zhang • 0
3
votes
3
replies
2.4k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.9 years ago • updated 3.8 years ago enricoferrero ▴ 680
2
votes
3
replies
1.8k
views
scater::plotHeatmap with swap_rownames gives error
scater
3.9 years ago enricoferrero ▴ 680
2
votes
2
replies
2.1k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
4.2 years ago doliv071 • 0
2
votes
3
replies
1.9k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.6 years ago by ▴ 160 • written 4.6 years ago by • 0
3
votes
2
replies
3.4k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.6 years ago camerond • 0
4
votes
5
replies
3.6k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.7 years ago by ★ 29k • written 4.7 years ago by ▴ 680
2
votes
7
replies
4.0k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 3.8 years ago by ★ 29k • written 4.8 years ago by ▴ 40
0
votes
0
replies
1.2k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.8 years ago hamza_karakurt ▴ 60
3
votes
3
replies
3.1k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 60
5
votes
5
replies
2.3k
views
Running NMF for single cell
NMF scater
4.9 years ago lirongrossmann ▴ 50
0
votes
1
reply
1.4k
views
Change annotation colors plotHeatmap
scater plotHeatmap
5.0 years ago simone.avesani22 • 0
5
votes
4
replies
8.4k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 680
3
votes
1
reply
1.7k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 5.2 years ago by ★ 29k • written 5.2 years ago by ★ 4.9k
0
votes
1
reply
2.1k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
0
votes
4
replies
1.8k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ★ 2.0k
2
votes
4
replies
3.5k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 4.6 years ago by • 0 • written 5.5 years ago by • 0
0
votes
1
reply
1.7k
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 5.8 years ago by ★ 29k • written 5.8 years ago by • 0
4
votes
1
reply
1.6k
views
could not find function "plotQC" in scater package
scater
updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 20
2
votes
1
reply
2.8k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 60
4
votes
4
replies
3.5k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 670
4
votes
4
replies
2.2k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
3
votes
7
replies
2.8k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
1
vote
4
replies
2.2k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
0
votes
7
replies
3.0k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
6.2 years ago Bogdan ▴ 670
0
votes
1
reply
1.2k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
6.2 years ago hamza_karakurt ▴ 60
2
votes
1
reply
1.6k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 350
2
votes
4
replies
4.7k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 3.4 years ago by • 0 • written 6.4 years ago by ▴ 10
8
votes
4
replies
3.8k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 60
2
votes
3
replies
2.3k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 10
4
votes
5
replies
2.5k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 60
7
votes
3
replies
4.5k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.4 years ago by ★ 29k • written 6.4 years ago by ▴ 10
98 results • Page 1 of 2
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Answer: ROAST compare results with complex design by James W. MacDonald 68k
You are specifying that the last column of your design should be used as the contrast. You should instead use `contrast[,1]`, which will us…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Yes. You can infer that by figuring out what each coefficient measures. Here is your design matrix: ``` > targets ID Name phase G…
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by snijesh ▴ 200
I would like to clarify whether the command `res <- results(dds, name = "phaseLP.conditionTreated")` is the correct approach to generate …
Comment: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Not sure I understand. You ask how to do something and then show how one would do so.
Comment: DiffBind getting Fold values of near 0 by littlefishes20 ▴ 10
Same issues. All peaks return to a fold near 0, although they are significant when visualizing in IGV. Please find the MAplot and volcanoPl…
Votes
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
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