Showing : Scran • reset
2
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209
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 25 days ago by ★ 4.0k • written 25 days ago by ★ 1.5k
0
votes
3
replies
385
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scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 3 months ago by ★ 4.0k • written 3 months ago by • 0
1
vote
2
replies
741
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
4 months ago ruba-mahmoud • 0
0
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1
reply
340
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 7 months ago by ★ 4.0k • written 7 months ago by • 0
0
votes
2
replies
782
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
10 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
replies
5.1k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 10 months ago by ▴ 740 • written 10 months ago by ★ 1.5k
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
10 months ago Lluís Revilla Sancho ▴ 730
0
votes
2
replies
687
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
12 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
replies
636
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
15 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 20 months ago by 65k • written 20 months ago by ▴ 10
1
vote
1
reply
777
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
3
votes
3
replies
1.1k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
22 months ago • updated 20 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 2.0 years ago by ▴ 770 • written 2.0 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
909
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.2 years ago msn ▴ 10
2
votes
2
replies
993
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Block weights in scran::pairwiseTTests
scran
2.4 years ago Angelos Armen • 0
1
vote
1
reply
1.1k
views
scran computeSumFactors showing error
scran single cell
updated 2.4 years ago by ★ 28k • written 2.4 years ago by • 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
2
votes
2
replies
1.7k
views
loading scran package
scran installation
3.2 years ago TJ • 0
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
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
0
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0
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752
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
965
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 3.5 years ago by ★ 28k • written 3.5 years ago by • 0
1
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1
reply
1.8k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 3.6 years ago by ★ 28k • written 3.6 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
6.0k
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
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
9
votes
4
replies
5.0k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 40
0
votes
4
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1.3k
views
scran's quickCluster error
scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ★ 4.0k
7
votes
5
replies
2.4k
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
4.7k
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
950
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
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
1
vote
1
reply
816
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
0
votes
5
replies
3.1k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.5 years ago by 25k • written 4.5 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 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
3
replies
913
views
k argument in buildSNNGraph
scran
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.7 years ago by ★ 28k • written 4.7 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 4.7 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
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
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
0
votes
7
replies
2.1k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.8 years ago Bogdan ▴ 670
0
votes
1
reply
820
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
3
votes
2
replies
1.1k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 4.9 years ago by ★ 28k • written 4.9 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 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
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
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 20
50 results • Page 1 of 1
Recent ...
Replies
Comment: DESeq filtering specific to contrasts by Carlin95 • 0
Thanks for clarifying. Could I ask maybe one more thing for my sanity? Let's say you had a multi-factor experiment with contrasts including…
Comment: FilterByExpr low counts with small sample size by Jonathan ▴ 10
Thank you for your answer; However, I have some follow-up question. Following up in In your [1-2-3 article][1], you say that > "... the …
Comment: DESeq2 a lot of genes showing up as differentially expressed that only have 1 sa by Seyram M. • 0
Thank you very much for your reply! I will do so. Kind regards, Seyram
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0` by isaac.vock • 0
Thank you for your response. I can confirm that setting `-t exon` and/or removing `-s 1` and adding `-O` has no impact on the number of suc…
Comment: Error retrieving ensembl gene id using biomaRt... by James W. MacDonald 65k
Or that. ;-D
Votes
Install/Switch between multiple versions of R, Rstudio, and Bioconductor
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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