Showing : SCRAN • reset
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301
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
3 months ago Lluís Revilla Sancho ▴ 760
0
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5
replies
601
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 5 months ago by ▴ 740 • written 5 months ago by ▴ 760
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0
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228
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Differential Gene Wrapper for Propotion of Detected
scran
5 months ago Dario Strbenac ★ 1.5k
0
votes
4
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620
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
6 months ago vohara4 • 0
1
vote
2
replies
437
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
7 months ago ATpoint ★ 4.6k
2
votes
1
reply
558
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 8 months ago by ★ 4.6k • written 8 months ago by ★ 1.5k
0
votes
3
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922
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 11 months ago by ★ 4.6k • written 11 months ago by • 0
1
vote
2
replies
1.5k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
12 months ago ruba-mahmoud • 0
0
votes
1
reply
691
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 15 months ago by ★ 4.6k • written 15 months ago by • 0
0
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2
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1.3k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
18 months ago Lluís Revilla Sancho ▴ 760
2
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2
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9.8k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 18 months ago by ▴ 740 • written 18 months ago by ★ 1.5k
2
votes
3
replies
1.7k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
18 months ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.1k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
20 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
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937
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
24 months ago r_grau ▴ 10
4
votes
3
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2.1k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.4 years ago by 67k • written 2.4 years ago by ▴ 10
1
vote
1
reply
1.1k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 2.5 years ago by ★ 4.6k • written 2.5 years ago by • 0
3
votes
3
replies
1.4k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
2.5 years ago • updated 2.4 years ago matthias-doering ▴ 40
2
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by • 0
2
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2
replies
1.6k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.8 years ago behr201 • 0
1
vote
2
replies
1.2k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.8 years ago msn ▴ 10
2
votes
2
replies
1.2k
views
Block weights in scran::pairwiseTTests
scran
3.1 years ago Angelos Armen • 0
1
vote
1
reply
1.4k
views
scran computeSumFactors showing error
scran single cell
updated 3.1 years ago by ★ 28k • written 3.1 years ago by • 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.2 years ago • updated 3.1 years ago enricoferrero ▴ 660
2
votes
2
replies
2.2k
views
loading scran package
scran installation
3.8 years ago TJ • 0
5
votes
6
replies
2.1k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.8 years ago by ★ 28k • written 3.9 years ago by • 0
4
votes
5
replies
2.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 660
0
votes
0
replies
971
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.1 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.2k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
1
vote
1
reply
2.3k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
2
votes
3
replies
2.2k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
5
votes
4
replies
7.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 660
2
votes
6
replies
1.4k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
9
votes
4
replies
5.9k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
0
votes
4
replies
1.6k
views
scran's quickCluster error
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
3
votes
1
reply
1.2k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ★ 4.6k
7
votes
5
replies
3.2k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
7
votes
3
replies
6.6k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 40
0
votes
3
replies
1.2k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 10
2
votes
1
reply
2.4k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 60
1
vote
1
reply
970
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.2 years ago by ★ 28k • written 5.2 years ago by • 0
0
votes
5
replies
3.4k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 5.2 years ago by 25k • written 5.2 years ago by ▴ 10
1
vote
2
replies
1.5k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 20
2
votes
1
reply
1.6k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
1
vote
3
replies
1.1k
views
k argument in buildSNNGraph
scran
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
5
replies
1.9k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
4
votes
4
replies
3.1k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 670
4
votes
4
replies
1.9k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
3
votes
7
replies
2.4k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
1
vote
4
replies
1.8k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 670
0
votes
7
replies
2.6k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.5 years ago Bogdan ▴ 670
50 results • Page 1 of 1
Recent ...
Replies
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
Since the intra-block correlation is negative, it would be best to remove `block` from the model. My experience with genetically identical…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by anna.cot.anna.cot ▴ 30
Thank you! This is actually quite close to my real dataset. I simplified the names to make it easier as an example, but I have now correcte…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Tim Peters ▴ 200
Hi Xiaofei, Is it possible to generate a matrix of beta values or M-values with rownames as probe IDs from this data? If so, cpg.annotate(…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by Gordon Smyth 52k
That looks basically correct, although the terms that you are inputing to `makeContrasts` do not match the condition names in the targets f…
Comment: Normalizing batch effects using technical replicates for DGE analysis between tw by James W. MacDonald 67k
Oh, right. There's two ways to enter code. If you are in the middle of a sentence and you want to include a function name, you wrap the nam…
Votes
Answer: nightmare to make custom txdb for genomes from ToxoDB
Comment: nightmare to make custom txdb for genomes from ToxoDB
Answer: Normalizing batch effects using technical replicates for DGE analysis between tw
Answer: nightmare to make custom txdb for genomes from ToxoDB
A: Advice on correcting for batch effect using DESeq2
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