Showing : SCRAN • reset
1
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3
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138
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Incosistencies in buildSNNGraph() function
scran seurat
written 5 days ago by • 0
0
votes
2
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1.1k
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Memory issue while using "quickcluster" and "computeSumFactors" functions on single cell RNA seq dataset with 7-9 lac cells
scran
updated 7 months ago by ★ 5.0k • written 8 months ago by • 0
1
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2
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1.5k
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Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors generic_find_knn scran quickCluster
9 months ago Arctic • 0
2
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2
replies
1.2k
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SingleR with multiple single cell references
SingleR scran
11 months ago • updated 9 months ago maltethodberg ▴ 180
0
votes
0
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1000
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
16 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
1.1k
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 18 months ago by ▴ 760 • written 18 months ago by ▴ 760
0
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0
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502
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Differential Gene Wrapper for Propotion of Detected
scran
19 months ago Dario Strbenac ★ 1.6k
0
votes
4
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1.3k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
1
vote
2
replies
835
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
21 months ago ATpoint ★ 5.0k
2
votes
1
reply
1.1k
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 22 months ago by ★ 5.0k • written 22 months ago by ★ 1.6k
0
votes
3
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1.6k
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scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 2.0 years ago by ★ 5.0k • written 2.0 years ago by • 0
1
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2
replies
2.1k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
2.1 years ago ruba-mahmoud • 0
0
votes
1
reply
1.2k
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Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 2.4 years ago by ★ 5.0k • written 2.4 years ago by • 0
0
votes
2
replies
2.0k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.6 years ago Lluís Revilla Sancho ▴ 760
2
votes
2
replies
11k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 2.6 years ago by ▴ 760 • written 2.6 years ago by ★ 1.5k
2
votes
3
replies
2.2k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.6 years ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.7k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.8 years ago Assa Yeroslaviz ★ 1.5k
1
vote
0
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1.4k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
3.0 years ago r_grau ▴ 10
4
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3
replies
2.8k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
1
vote
1
reply
1.4k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
3
votes
3
replies
2.0k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
3.6 years ago • updated 3.4 years ago matthias-doering ▴ 40
2
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1
reply
2.0k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
2
votes
2
replies
2.3k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.9 years ago behr201 • 0
1
vote
2
replies
1.6k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.9 years ago msn ▴ 10
2
votes
2
replies
1.6k
views
Block weights in scran::pairwiseTTests
scran
4.2 years ago Angelos Armen • 0
1
vote
1
reply
1.8k
views
scran computeSumFactors showing error
scran single cell
updated 4.2 years ago by ★ 29k • written 4.2 years ago by • 0
3
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3
replies
2.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.2 years ago enricoferrero ▴ 680
2
votes
2
replies
2.9k
views
loading scran package
scran installation
4.9 years ago TJ • 0
5
votes
6
replies
2.8k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.9 years ago by ★ 29k • written 4.9 years ago by • 0
4
votes
5
replies
4.0k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 680
0
votes
0
replies
1.4k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
5.2 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.5k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 5.2 years ago by ★ 29k • written 5.2 years ago by • 0
1
vote
1
reply
2.8k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
2
votes
3
replies
2.9k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 5.4 years ago by ★ 29k • written 5.4 years ago by • 0
5
votes
4
replies
9.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 680
2
votes
6
replies
2.0k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.6 years ago by ★ 29k • written 5.6 years ago by • 0
9
votes
4
replies
7.2k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 5.6 years ago by ★ 29k • written 5.6 years ago by ▴ 40
0
votes
4
replies
2.1k
views
scran's quickCluster error
scran
updated 5.7 years ago by ★ 29k • written 5.7 years ago by • 0
3
votes
1
reply
1.6k
views
Output lfc for Wilcox-based findMarkers
scran
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ★ 5.0k
7
votes
5
replies
4.9k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 40
7
votes
3
replies
8.4k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 40
0
votes
3
replies
1.7k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 10
2
votes
1
reply
3.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 60
1
vote
1
reply
1.3k
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 6.3 years ago by ★ 29k • written 6.3 years ago by • 0
0
votes
5
replies
3.9k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 6.3 years ago by 25k • written 6.3 years ago by ▴ 10
1
vote
2
replies
2.0k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 6.3 years ago by ★ 29k • written 6.3 years ago by ▴ 20
2
votes
1
reply
2.2k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
1
vote
3
replies
1.5k
views
k argument in buildSNNGraph
scran
updated 6.4 years ago by ★ 29k • written 6.4 years ago by • 0
1
vote
5
replies
2.5k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 6.5 years ago by ★ 29k • written 6.5 years ago by • 0
4
votes
4
replies
3.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 670
100 results • Page 1 of 2
Recent ...
Replies
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
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