Showing : SCRAN • reset
1
vote
2
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177
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
25 days ago • updated 24 days ago ATpoint ★ 4.1k
2
votes
1
reply
256
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 7 weeks ago by ★ 4.1k • written 8 weeks ago by ★ 1.5k
0
votes
3
replies
475
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
1
vote
2
replies
902
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
5 months ago ruba-mahmoud • 0
0
votes
1
reply
385
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Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 8 months ago by ★ 4.1k • written 8 months ago by • 0
0
votes
2
replies
859
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
11 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
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5.7k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 11 months ago by ▴ 740 • written 11 months ago by ★ 1.5k
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
11 months ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
753
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
13 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
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688
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
16 months ago r_grau ▴ 10
4
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3
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1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months ago by ▴ 10
1
vote
1
reply
825
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 22 months ago by ★ 4.1k • written 22 months ago by • 0
3
votes
3
replies
1.2k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
23 months ago • updated 21 months ago matthias-doering ▴ 40
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
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago behr201 • 0
1
vote
2
replies
943
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.3 years ago • updated 2.2 years ago msn ▴ 10
2
votes
2
replies
1.0k
views
Block weights in scran::pairwiseTTests
scran
2.5 years ago Angelos Armen • 0
1
vote
1
reply
1.1k
views
scran computeSumFactors showing error
scran single cell
updated 2.5 years ago by ★ 28k • written 2.5 years ago by • 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.6 years ago enricoferrero ▴ 660
2
votes
2
replies
1.8k
views
loading scran package
scran installation
3.3 years ago TJ • 0
5
votes
6
replies
1.7k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 660
0
votes
0
replies
784
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
1
vote
1
reply
985
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 3.5 years ago by ★ 28k • written 3.6 years ago by • 0
1
vote
1
reply
1.9k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
9
votes
4
replies
5.1k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
0
votes
4
replies
1.4k
views
scran's quickCluster error
scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
3
votes
1
reply
1.1k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ★ 4.1k
7
votes
5
replies
2.5k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
7
votes
3
replies
5.0k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.1 years ago by ▴ 40
0
votes
3
replies
976
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 10
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 50
1
vote
1
reply
835
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
5
replies
3.2k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 10
1
vote
2
replies
1.3k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 20
2
votes
1
reply
1.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
3
replies
938
views
k argument in buildSNNGraph
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
5
replies
1.7k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.8 years ago by ★ 28k • written 4.8 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 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.9 years ago by ★ 28k • written 4.9 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
1
reply
841
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
3
votes
2
replies
1.2k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: all variables in design formula must be columns in colData (Deseq2) error by Galina • 0
thank you!
Comment: all variables in design formula must be columns in colData (Deseq2) error by ATpoint ★ 4.1k
coldata_rat <- data.frame(conditions=..., batch=...)
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by robersy • 0
Thank you all for your comments. I will follow your suggestions.
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Hi Michael, thanks a lot for your prompt reply! Not sure if this is appropriate or if you are the right person to ask -- is there anything…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by Ken C • 0
Well, if I look at genes with baseMean>50, then the relative absolute difference in log2FoldChange (say over the absolute log2FoldChange of…
Votes
biomaRt not working - lazy table error
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
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