Showing : SCRAN • reset
1
vote
2
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175
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
24 days ago • updated 23 days ago ATpoint ★ 4.1k
2
votes
1
reply
254
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 7 weeks ago by ★ 4.1k • written 7 weeks ago by ★ 1.5k
0
votes
3
replies
474
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
895
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
5 months ago ruba-mahmoud • 0
0
votes
1
reply
384
views
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
856
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
11 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
replies
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
750
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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687
views
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
votes
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
824
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 • updated 2.5 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
783
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 4.0 years ago by ▴ 40
0
votes
3
replies
975
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.1 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
937
views
k argument in buildSNNGraph
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
1
vote
5
replies
1.6k
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
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
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
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
840
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
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.2 years ago by • 0 • written 5.1 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Comment: DESeq2- Mysterious interaction suppresses DEGs by shaunpeterson • 0
The images I tried to attach didn't attach. Here is the PCA (MDS) of all the samples, with the Cortex outlier highlighed. ![enter image de…
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Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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