Showing : Scater • reset
0
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4
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255
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 days ago vohara4 • 0
3
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3
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645
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 3 months ago by ▴ 160 • written 3 months ago by • 0
2
votes
1
reply
332
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 3 months ago by ★ 4.2k • written 3 months ago by ★ 1.5k
3
votes
3
replies
575
views
plotUMAP Gene Set Faceted
scater
updated 5 months ago by ▴ 160 • written 5 months ago by ★ 1.5k
1
vote
1
reply
336
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 5 months ago by ▴ 160 • written 5 months ago by ★ 1.5k
1
vote
7
replies
7.3k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 4 months ago by 16k • written 7 months ago by ▴ 10
0
votes
3
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1.2k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 10 months ago by ★ 4.2k • written 10 months ago by • 0
0
votes
6
replies
966
views
plotHeatmap annotation error
plotHeatmap scater
12 months ago Alina • 0
1
vote
0
replies
1.5k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
17 months ago cathalgking ▴ 10
0
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1
reply
743
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 17 months ago by ▴ 160 • written 17 months ago by ▴ 10
1
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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
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4
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2.1k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 23 months ago by ★ 28k • written 23 months ago by ▴ 40
3
votes
2
replies
1.8k
views
FeaturePlot in scater
scater OSCA
2.0 years ago Guandong Shang ▴ 40
5
votes
4
replies
1.8k
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 ▴ 780 • written 2.2 years ago by • 0
0
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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 2.4 years ago by ▴ 160 • written 2.4 years ago by • 0
2
votes
7
replies
1.8k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 2.4 years ago by ▴ 280 • written 2.4 years ago by ▴ 10
1
vote
2
replies
986
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.4 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
1.8k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.7 years ago enricoferrero ▴ 660
2
votes
3
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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
3.1 years ago • updated 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 ▴ 160 • written 3.4 years ago by • 0
3
votes
2
replies
2.4k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.4 years ago camerond • 0
4
votes
5
replies
2.4k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 660
2
votes
7
replies
2.8k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.6 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
votes
0
replies
805
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
3.7 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 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 60
5
votes
5
replies
1.8k
views
Running NMF for single cell
NMF scater
3.7 years ago lirongrossmann ▴ 50
0
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1
reply
1.1k
views
Change annotation colors plotHeatmap
scater plotHeatmap
3.8 years ago simone.avesani22 • 0
5
votes
4
replies
6.3k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 660
3
votes
1
reply
1.2k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ★ 4.2k
0
votes
1
reply
1.3k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.2 years ago by ★ 28k • written 4.2 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 4.3 years ago by ★ 28k • written 4.3 years ago by ★ 2.0k
2
votes
4
replies
2.5k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.4 years ago by • 0 • written 4.3 years ago by • 0
0
votes
1
reply
1.1k
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
4
votes
1
reply
1.3k
views
could not find function "plotQC" in scater package
scater
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 20
2
votes
1
reply
2.1k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 60
4
votes
4
replies
2.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
4
votes
4
replies
1.6k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
3
votes
7
replies
2.1k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
1
vote
4
replies
1.6k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 670
0
votes
7
replies
2.3k
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
874
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.1 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 ★ 28k • written 5.1 years ago by ▴ 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 2.3 years ago by • 0 • written 5.2 years ago by ▴ 10
8
votes
4
replies
2.5k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 60
2
votes
3
replies
1.7k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.2 years ago by ★ 28k • written 5.2 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 5.2 years ago by ▴ 150 • written 5.2 years ago by ▴ 60
7
votes
3
replies
3.4k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Trouble Installing DADA2 (warning: R new user) by shepherl 3.9k
As far as this ERROR for Bioc requires R version, Bioconductor is closely tied to an R release. Depending if you tried to use a premade s…
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No, this is a contrast of estimated coefficient (e.g. the Wald test).
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Got it. So then I'll take off DESeq2 as its mostly a downstream question. You may need to direct the fgsea developer to the thread. When yo…
Comment: Ranking the GSEA Results by V_Vibes • 0
I have actually used the "fgsea" Bioconductor package which is used for GSEA. Thanks for pointing that out. I have edited that in the origi…
Comment: Ranking the GSEA Results by V_Vibes • 0
The idea was inspired by people ranking the DEGs for preranked GSEA using their log2FC * (-log10 p-value). Also, the GSEA results I am gett…
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Error in `$<-.data.frame`(`*tmp*`, "dispersion", value = NA)
ChiPseeker package: plotAnnoPie identical colors for peakAnnoList features
Comment: How to get the DMR?
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
Answer: Using both voom and removeBatchEffect, will they double adjust the data or is it
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