Showing : Scater • reset
3
votes
3
replies
357
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 4 weeks ago by ▴ 160 • written 4 weeks ago by • 0
2
votes
1
reply
218
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 4 weeks ago by ★ 4.0k • written 4 weeks ago by ★ 1.5k
3
votes
3
replies
330
views
plotUMAP Gene Set Faceted
scater
updated 12 weeks ago by ▴ 160 • written 12 weeks ago by ★ 1.5k
1
vote
1
reply
230
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 12 weeks ago by ▴ 160 • written 12 weeks ago by ★ 1.5k
1
vote
7
replies
6.4k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 7 weeks ago by 16k • written 5 months ago by ▴ 10
0
votes
3
replies
1.1k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
6
replies
855
views
plotHeatmap annotation error
plotHeatmap scater
10 months ago Alina • 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
641
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 15 months ago by ▴ 160 • written 15 months ago by ▴ 10
1
vote
2
replies
1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
18 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 20 months ago by ★ 28k • written 21 months ago by ▴ 40
3
votes
2
replies
1.6k
views
FeaturePlot in scater
scater OSCA
22 months ago Guandong Shang ▴ 40
5
votes
4
replies
1.6k
views
scater runUMAP
scater runUMAP
2.1 years ago • updated 2.0 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
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 2.2 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
913
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.2 years ago msn ▴ 10
1
vote
2
replies
1.1k
views
More than 3 dimensions in runTSNE
dimensions scater runTSNE
2.4 years ago jianhai.zhang • 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
2
votes
3
replies
1.1k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.5 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 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
3
votes
2
replies
2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
2
votes
7
replies
2.6k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.4 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
votes
0
replies
757
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
2.3k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 60
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF scater
3.5 years ago lirongrossmann ▴ 40
0
votes
1
reply
1.0k
views
Change annotation colors plotHeatmap
scater plotHeatmap
3.6 years ago simone.avesani22 • 0
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 ★ 28k • written 3.7 years ago by ▴ 660
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.8 years ago by ★ 28k • written 3.9 years ago by ★ 4.0k
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 4.1 years ago by ★ 2.0k
2
votes
4
replies
2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.2 years ago by • 0 • written 4.1 years ago by • 0
0
votes
1
reply
991
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 20
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.5 years ago by ★ 28k • written 4.5 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
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
7
replies
1.9k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
0
votes
7
replies
2.1k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.8 years ago Bogdan ▴ 670
0
votes
1
reply
823
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
2
votes
1
reply
1.1k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 350
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.1 years ago by • 0 • written 5.0 years ago by ▴ 10
8
votes
4
replies
2.2k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 50
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
4
votes
5
replies
1.7k
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
3.2k
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 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
50 results • Page 1 of 1
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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by marka • 0
As a single dad in Australia, finding time to unwind is rare, but [Lincoln Casino][1] has become my go-to escape after putting the kids to …
Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k
You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k
Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…
Comment: get BM error by James W. MacDonald 65k
I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…
Comment: get BM error by Fara • 0
Thank you for your response. The primary reason for translating Ensembl IDs into Entrez Gene IDs is to perform KEGG (Kyoto Encyclopedia of…
Votes
Answer: get BM error
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
Comment: Different Shrunk Log2FC according with reference
Reproducibility issue with scran together with lapply and BiocParallel
C: SGSeq: moving toward diffex from SGSeq analysis
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