Showing : Scater • reset
0
votes
16
replies
2.4k
views
How does newSCESet calculate expression matrix
scater
updated 6.9 years ago by ▴ 90 • written 6.9 years ago by • 0
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
3
votes
9
replies
4.1k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
1
vote
8
replies
2.3k
views
SC3_estimate_k formatting error?
sc3 scater
updated 6.4 years ago by ▴ 150 • written 6.5 years ago by ▴ 10
0
votes
7
replies
1.7k
views
error when installing beachmat
beachmat scater
updated 6.3 years ago by ▴ 10 • written 6.4 years ago by • 0
4
votes
7
replies
6.3k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater
updated 6.8 years ago by ▴ 40 • written 7.0 years ago by • 0
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
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
7
replies
6.5k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 8 weeks ago by 16k • written 5 months ago by ▴ 10
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
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
6
replies
1.7k
views
Scater package PlotExpression
scater
5.7 years ago mayank.geit89 • 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
5
votes
6
replies
2.7k
views
Error when merging SCESet objects
scater single-cell
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
0
votes
6
replies
862
views
plotHeatmap annotation error
plotHeatmap scater
10 months ago Alina • 0
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
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
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF scater
3.5 years ago lirongrossmann ▴ 40
2
votes
5
replies
1.9k
views
sc3_prepare function error
sc3 scater single-cell single cell
updated 7.2 years ago by ▴ 150 • written 7.2 years ago by ★ 1.5k
3
votes
5
replies
1.3k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
5.6 years ago hamza_karakurt ▴ 50
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
5
replies
1.6k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 30
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
2
votes
5
replies
3.8k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 20 months ago by ▴ 60 • written 5.2 years ago by ▴ 50
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
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
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
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
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
8
votes
4
replies
2.3k
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
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
5
votes
4
replies
1.6k
views
scater runUMAP
scater runUMAP
2.1 years ago jianhai.zhang • 0
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
0
votes
4
replies
4.8k
views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
updated 6.1 years ago by • 0 • written 7.0 years ago by ▴ 70
3
votes
4
replies
1.8k
views
Scran normalization error with computeSumFactors
scran scater
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
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 5.1 years ago by ▴ 10
3
votes
3
replies
7.1k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.8 years ago by 25k • written 6.0 years ago by ▴ 10
2
votes
3
replies
1.2k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.5 years ago enricoferrero ▴ 660
1
vote
3
replies
1.1k
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
0
votes
3
replies
1.1k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 8 months ago by ★ 4.0k • written 8 months ago by • 0
3
votes
3
replies
2.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater LoomR SCopeloomR
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 20
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3 scater scRNAseq
updated 7.1 years ago by ▴ 150 • written 7.1 years ago by ★ 1.5k
3
votes
3
replies
344
views
plotUMAP Gene Set Faceted
scater
updated 12 weeks ago by ▴ 160 • written 12 weeks ago by ★ 1.5k
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 6.5 years ago by ▴ 90 • written 6.5 years ago by • 0
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
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
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
50 results • Page 1 of 1
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Comment: Why p value inconsistent when using different number of pathway score? by Chris • 0
Hi Robert, if two conditions don't have hundreds of differential express genes ( in some conditions such as peripheral blood Alzheimer vs n…
Answer: Dominance Index for Shotgun Metagenomics Data by Leo Lahti ▴ 40
1. Note that Simpson's dominance index (\lambda) is a different index than inverse Simpson (1/\lambda) or reciprocal Simpson (1-\lambda). T…
Comment: Math expression in shapeCustom legend in EnhancedVolcano by pl23 • 0
Thank you very much - that worked perfectly! Word of warning to those who try this: it screws up the other legends because of the markdown …
Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Votes
Answer: Dominance Index for Shotgun Metagenomics Data
Answer: Math expression in shapeCustom legend in EnhancedVolcano
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
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