Showing : scater • reset
0
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4
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624
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
3
votes
3
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1.4k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 9 months ago by ▴ 160 • written 9 months ago by • 0
2
votes
1
reply
563
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 9 months ago by ★ 4.6k • written 9 months ago by ★ 1.5k
3
votes
3
replies
1.2k
views
plotUMAP Gene Set Faceted
scater
updated 10 months ago by ▴ 160 • written 10 months ago by ★ 1.5k
1
vote
1
reply
566
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 10 months ago by ▴ 160 • written 10 months ago by ★ 1.5k
1
vote
7
replies
8.6k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 9 months ago by 16k • written 13 months ago by ▴ 10
0
votes
3
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1.6k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
votes
6
replies
1.2k
views
plotHeatmap annotation error
plotHeatmap scater
18 months ago Alina • 0
1
vote
0
replies
1.9k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
22 months ago cathalgking ▴ 10
0
votes
1
reply
948
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 23 months ago by ▴ 160 • written 23 months ago by ▴ 10
1
vote
2
replies
1.5k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.2 years ago Guandong Shang ▴ 40
0
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4
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2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.4 years ago by ★ 28k • written 2.4 years ago by ▴ 40
3
votes
2
replies
2.1k
views
FeaturePlot in scater
scater OSCA
2.5 years ago Guandong Shang ▴ 40
5
votes
4
replies
2.2k
views
scater runUMAP
scater runUMAP
2.7 years ago jianhai.zhang • 0
2
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
0
votes
6
replies
3.4k
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 2.8 years ago by ▴ 160 • written 2.9 years ago by • 0
2
votes
7
replies
2.1k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 2.8 years ago by ▴ 280 • written 2.8 years ago by ▴ 10
1
vote
2
replies
1.2k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.8 years ago msn ▴ 10
1
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2
replies
1.4k
views
More than 3 dimensions in runTSNE
dimensions scater runTSNE
3.1 years ago jianhai.zhang • 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.2 years ago • updated 3.1 years ago enricoferrero ▴ 660
2
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3
replies
1.5k
views
scater::plotHeatmap with swap_rownames gives error
scater
3.2 years ago enricoferrero ▴ 660
2
votes
2
replies
1.7k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
3.5 years ago doliv071 • 0
2
votes
3
replies
1.6k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.9 years ago by ▴ 160 • written 3.9 years ago by • 0
3
votes
2
replies
2.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.9 years ago camerond • 0
4
votes
5
replies
2.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 660
2
votes
7
replies
3.3k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 3.1 years ago by ★ 28k • written 4.1 years ago by ▴ 40
0
votes
0
replies
973
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.1 years ago hamza_karakurt ▴ 60
3
votes
3
replies
2.7k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 60
5
votes
5
replies
2.0k
views
Running NMF for single cell
NMF scater
4.2 years ago lirongrossmann ▴ 50
0
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1
reply
1.3k
views
Change annotation colors plotHeatmap
scater plotHeatmap
4.3 years ago simone.avesani22 • 0
5
votes
4
replies
7.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 660
3
votes
1
reply
1.4k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ★ 4.6k
0
votes
1
reply
1.7k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
4
replies
1.5k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ★ 2.0k
2
votes
4
replies
2.9k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.9 years ago by • 0 • written 4.8 years ago by • 0
0
votes
1
reply
1.3k
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
4
votes
1
reply
1.4k
views
could not find function "plotQC" in scater package
scater
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 20
2
votes
1
reply
2.4k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 60
4
votes
4
replies
3.1k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 670
4
votes
4
replies
1.9k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
3
votes
7
replies
2.4k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
1
vote
4
replies
1.8k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
0
votes
7
replies
2.6k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.5 years ago Bogdan ▴ 670
0
votes
1
reply
1.0k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.5 years ago hamza_karakurt ▴ 60
2
votes
1
reply
1.3k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 350
2
votes
4
replies
4.1k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.7 years ago by • 0 • written 5.7 years ago by ▴ 10
8
votes
4
replies
3.0k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 60
2
votes
3
replies
1.9k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
4
votes
5
replies
2.1k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.7 years ago by ▴ 150 • written 5.7 years ago by ▴ 60
7
votes
3
replies
3.9k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Cross-validation with multiple control subgroups in limma by Gordon Smyth 52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Votes
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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