Showing : Scran • reset
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418
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
4 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
674
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 7 months ago by ▴ 750 • written 7 months ago by ▴ 760
0
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0
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268
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Differential Gene Wrapper for Propotion of Detected
scran
7 months ago Dario Strbenac ★ 1.6k
0
votes
4
replies
700
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
8 months ago vohara4 • 0
1
vote
2
replies
487
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
9 months ago ATpoint ★ 4.6k
2
votes
1
reply
644
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 10 months ago by ★ 4.6k • written 10 months ago by ★ 1.6k
0
votes
3
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1.0k
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 13 months ago by ★ 4.6k • written 13 months ago by • 0
1
vote
2
replies
1.6k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
14 months ago ruba-mahmoud • 0
0
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1
reply
780
views
Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 17 months ago by ★ 4.6k • written 17 months ago by • 0
0
votes
2
replies
1.4k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
20 months ago Lluís Revilla Sancho ▴ 760
2
votes
2
replies
10k
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scran ScoreMarkers throws a warning
scoreMarkers scran
updated 20 months ago by ▴ 750 • written 20 months ago by ★ 1.5k
2
votes
3
replies
1.8k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
20 months ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.2k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
22 months ago Assa Yeroslaviz ★ 1.5k
1
vote
0
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1.0k
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.1 years ago r_grau ▴ 10
4
votes
3
replies
2.2k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.5 years ago by 68k • written 2.5 years ago by ▴ 10
1
vote
1
reply
1.1k
views
setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
3
votes
3
replies
1.5k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
2.7 years ago • updated 2.5 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 2.9 years ago by ▴ 780 • written 2.9 years ago by • 0
2
votes
2
replies
1.7k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.0 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
3.0 years ago msn ▴ 10
2
votes
2
replies
1.3k
views
Block weights in scran::pairwiseTTests
scran
3.2 years ago Angelos Armen • 0
1
vote
1
reply
1.5k
views
scran computeSumFactors showing error
scran single cell
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
3
votes
3
replies
2.1k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.3 years ago enricoferrero ▴ 680
2
votes
2
replies
2.4k
views
loading scran package
scran installation
4.0 years ago TJ • 0
5
votes
6
replies
2.2k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
4
votes
5
replies
3.1k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 680
0
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0
replies
1.0k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.3 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.2k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.3 years ago by ★ 28k • written 4.3 years ago by • 0
1
vote
1
reply
2.4k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
2
votes
3
replies
2.3k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
5
votes
4
replies
7.4k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 680
2
votes
6
replies
1.5k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
9
votes
4
replies
6.2k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 40
0
votes
4
replies
1.7k
views
scran's quickCluster error
scran
updated 4.7 years ago by ★ 28k • written 4.8 years ago by • 0
3
votes
1
reply
1.3k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ★ 4.6k
7
votes
5
replies
3.5k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 40
7
votes
3
replies
6.9k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 40
0
votes
3
replies
1.3k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.9 years ago by ★ 28k • written 4.9 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 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 60
1
vote
1
reply
1.0k
views
Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
0
votes
5
replies
3.5k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 5.4 years ago by 25k • written 5.4 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
2
votes
1
reply
1.7k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
1
vote
3
replies
1.2k
views
k argument in buildSNNGraph
scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
1
vote
5
replies
2.0k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
4
votes
4
replies
3.2k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 670
4
votes
4
replies
1.9k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 670
3
votes
7
replies
2.5k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 670
1
vote
4
replies
1.9k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 670
0
votes
7
replies
2.7k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.7 years ago Bogdan ▴ 670
50 results • Page 1 of 1
Recent ...
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Comment: GSVA on RNAseq data by Robert Castelo ★ 3.4k
Hi Bob, I have not investigated whether a particular unit of expression works better than others, but using logTPM or logCPM units of expr…
Answer: Store Matrix in DataFrame Cell by James W. MacDonald 68k
Put it in a list and put the list in a column.
Comment: For some reason I can't update BiocManager to 3.20 by James W. MacDonald 68k
Please post output from starting R and then running `sessionInfo()` (as requested by the web form you use to post questions). I get ``` > …
Comment: p-value the same for different contrasts DESeq2 by caroline.zanchi • 0
It would be great if it were possible to do something similar using GlmGamPoi !
Comment: Web accessibility of Bioconductor.org by Sean Davis 21k
Added issue to website github repo: https://github.com/Bioconductor/bioconductor.org/issues/304
Votes
A: Rtracklayer fails to export TxDb as GFF3 without CDS
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Store Matrix in DataFrame Cell
Store Matrix in DataFrame Cell
A: how to extract Granges not overlapping with other ganges?
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