Showing : Scater • reset
8
votes
4
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2.2k
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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
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
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF scater
3.5 years ago lirongrossmann ▴ 40
5
votes
2
replies
5.8k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment sc3 scater
updated 6.4 years ago by ▴ 150 • written 6.4 years ago by ▴ 10
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
2
replies
1.6k
views
Accessing normalized counts
splatter singlecellexperiment scater
6.0 years ago luke.zappia ▴ 50
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
5
votes
4
replies
1.6k
views
scater runUMAP
scater runUMAP
2.0 years ago jianhai.zhang • 0
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
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 4.7 years ago by ★ 28k • written 4.8 years ago by ▴ 670
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
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
4
votes
5
replies
2.2k
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
4
votes
0
replies
3.4k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
7.6 years ago Aaron Lun ★ 28k
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
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
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 50
3
votes
3
replies
7.0k
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
3
votes
5
replies
1.2k
views
plotPlatePosition and plate_position
scater R singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
3
votes
3
replies
323
views
plotUMAP Gene Set Faceted
scater
updated 11 weeks ago by ▴ 160 • written 11 weeks ago by ★ 1.5k
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
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
3
votes
2
replies
1.6k
views
FeaturePlot in scater
scater OSCA
22 months ago Guandong Shang ▴ 40
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
3
votes
3
replies
334
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 25 days ago by ▴ 160 • written 26 days 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
3
votes
2
replies
3.1k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater simpleSingleCell workflows
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 70
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
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
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
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
2
votes
7
replies
2.5k
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
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
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
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater pca features
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
2
votes
2
replies
1.4k
views
scater error: invalid rownames length
scater
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
2
votes
5
replies
3.7k
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
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
2
votes
4
replies
3.5k
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
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
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
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
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
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ★ 4.0k
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
2
votes
2
replies
1.3k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
2.9 years ago • updated 2.8 years ago doliv071 • 0
2
votes
3
replies
1.1k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.5 years ago enricoferrero ▴ 660
2
votes
1
reply
209
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 25 days ago by ★ 4.0k • written 26 days ago by ★ 1.5k
2
votes
7
replies
1.7k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 2.1 years ago by ▴ 270 • written 2.2 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: Bioinformatics Laboratory Head in AI or machine learning (WEHI, Australia) by christianhilton64 • 0
I'm less familiar with the specifics of GSVA, but I'm curious about the overall goal of this analysis. Could you provide a high-level summa…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Robert Castelo ★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq by lonn • 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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