Showing : SCRAN • reset
0
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934
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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 3 months ago by ★ 4.9k • written 3 months ago by • 0
1
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2
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1.3k
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Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors generic_find_knn scran quickCluster
5 months ago Arctic • 0
2
votes
2
replies
943
views
SingleR with multiple single cell references
SingleR scran
6 months ago • updated 5 months ago maltethodberg ▴ 180
0
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0
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815
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
12 months ago Lluís Revilla Sancho ▴ 760
0
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5
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960
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 14 months ago by ▴ 760 • written 14 months ago by ▴ 760
0
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0
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380
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Differential Gene Wrapper for Propotion of Detected
scran
14 months ago Dario Strbenac ★ 1.6k
0
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4
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1.0k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
15 months ago vohara4 • 0
1
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2
replies
687
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
16 months ago ATpoint ★ 4.9k
2
votes
1
reply
891
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 17 months ago by ★ 4.9k • written 17 months ago by ★ 1.6k
0
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3
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1.3k
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 20 months ago by ★ 4.9k • written 20 months ago by • 0
1
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2
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1.9k
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
21 months ago ruba-mahmoud • 0
0
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1
reply
1.0k
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 2.0 years ago by ★ 4.9k • written 2.0 years ago by • 0
0
votes
2
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1.8k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.2 years ago Lluís Revilla Sancho ▴ 760
2
votes
2
replies
11k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 2.2 years ago by ▴ 760 • written 2.2 years ago by ★ 1.5k
2
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3
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2.0k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.3 years ago Lluís Revilla Sancho ▴ 760
0
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2
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1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.5 years ago Assa Yeroslaviz ★ 1.5k
1
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0
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1.2k
views
Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.7 years ago r_grau ▴ 10
4
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3
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2.6k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
1
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1
reply
1.3k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
3
votes
3
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1.8k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
3.2 years ago • updated 3.1 years ago matthias-doering ▴ 40
2
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1
reply
1.8k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
2
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2
replies
2.0k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.6 years ago behr201 • 0
1
vote
2
replies
1.4k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.6 years ago msn ▴ 10
2
votes
2
replies
1.5k
views
Block weights in scran::pairwiseTTests
scran
3.8 years ago Angelos Armen • 0
1
vote
1
reply
1.7k
views
scran computeSumFactors showing error
scran single cell
updated 3.8 years ago by ★ 29k • written 3.8 years ago by • 0
3
votes
3
replies
2.4k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.9 years ago enricoferrero ▴ 680
2
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2
replies
2.7k
views
loading scran package
scran installation
4.6 years ago TJ • 0
5
votes
6
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2.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.6 years ago by ★ 29k • written 4.6 years ago by • 0
4
votes
5
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3.7k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.7 years ago by ★ 29k • written 4.7 years ago by ▴ 680
0
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0
replies
1.2k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.9 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.4k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.9 years ago by ★ 29k • written 4.9 years ago by • 0
1
vote
1
reply
2.7k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 5.0 years ago by ★ 29k • written 5.0 years ago by • 0
2
votes
3
replies
2.6k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 5.1 years ago by ★ 29k • written 5.1 years ago by • 0
5
votes
4
replies
8.4k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 680
2
votes
6
replies
1.8k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 5.2 years ago by ★ 29k • written 5.2 years ago by • 0
9
votes
4
replies
6.9k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 40
0
votes
4
replies
1.9k
views
scran's quickCluster error
scran
updated 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
3
votes
1
reply
1.5k
views
Output lfc for Wilcox-based findMarkers
scran
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ★ 4.9k
7
votes
5
replies
4.5k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 40
7
votes
3
replies
8.0k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 40
0
votes
3
replies
1.5k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 5.5 years ago by ★ 29k • written 5.5 years ago by ▴ 10
2
votes
1
reply
2.8k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 60
1
vote
1
reply
1.2k
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.9 years ago by ★ 29k • written 5.9 years ago by • 0
0
votes
5
replies
3.7k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 5.9 years ago by 25k • written 5.9 years ago by ▴ 10
1
vote
2
replies
1.8k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 6.0 years ago by ★ 29k • written 6.0 years ago by ▴ 20
2
votes
1
reply
2.0k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
1
vote
3
replies
1.4k
views
k argument in buildSNNGraph
scran
updated 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
1
vote
5
replies
2.3k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 6.1 years ago by ★ 29k • written 6.1 years ago by • 0
4
votes
4
replies
3.5k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 6.1 years ago by ★ 29k • written 6.1 years ago by ▴ 670
4
votes
4
replies
2.3k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 6.2 years ago by ★ 29k • written 6.2 years ago by ▴ 670
99 results • Page 1 of 2
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Answer: How to construct a BSgenome object from a custom genome assembly using BSgenomeF by James W. MacDonald 68k
There is an example in the help page for `forgeBSgenomePkgFromTwobitFile`. Have you tried emulating that?
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What you describe sounds a good approach to me. I would also use sample weights (`sample.weights=TRUE` when running `voomLmFit`) and robust…
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I moved your post from an "answer" to a "comment". I don't know about `offst()` function, what is the scale or direction, or whether you a…
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@atpoint Should I first standardise data and then average replicates?
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Thans you @swbarnes2 for the answer. I can see why trying to include all three parameters might be difficult to interpret. But we're inte…
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