Showing : scran • reset
0
votes
2
replies
924
views
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
vote
2
replies
1.3k
views
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
933
views
SingleR with multiple single cell references
SingleR scran
6 months ago • updated 5 months ago maltethodberg ▴ 180
0
votes
0
replies
808
views
modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
11 months ago Lluís Revilla Sancho ▴ 760
0
votes
5
replies
954
views
modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 14 months ago by ▴ 760 • written 14 months ago by ▴ 760
0
votes
0
replies
376
views
Differential Gene Wrapper for Propotion of Detected
scran
14 months ago Dario Strbenac ★ 1.6k
0
votes
4
replies
1.0k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
15 months ago vohara4 • 0
1
vote
2
replies
681
views
Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
16 months ago ATpoint ★ 4.9k
2
votes
1
reply
885
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
votes
3
replies
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
vote
2
replies
1.9k
views
ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
21 months ago ruba-mahmoud • 0
0
votes
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
replies
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
votes
3
replies
2.0k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
2.3 years ago • updated 2.2 years ago Lluís Revilla Sancho ▴ 760
0
votes
2
replies
1.5k
views
Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.4 years ago Assa Yeroslaviz ★ 1.5k
1
vote
0
replies
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
votes
3
replies
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
vote
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
replies
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
votes
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
votes
2
replies
2.0k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.5 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 • updated 3.5 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
votes
2
replies
2.7k
views
loading scran package
scran installation
4.6 years ago TJ • 0
5
votes
6
replies
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
replies
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
votes
0
replies
1.2k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.8 years ago hamza_karakurt ▴ 60
1
vote
1
reply
1.4k
views
scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.8 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 5.0 years ago by ★ 29k • written 5.0 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 5.3 years ago by ★ 29k • written 5.3 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 5.9 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
2.2k
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
Recent ...
Replies
Comment: org.Ss.eg.db MAMDC4 maps to incorrect UNIPROT key by thundernight • 0
I'm actually having the same problem. [Spanish dictionary][1] [1]: https://spanishdictionary.cc
Comment: voomLmFit fitted log-CPM values by Gordon Smyth 52k
The fitted values are on the log2CPM scale. I would have told you if they were not! I think you may be getting confused by the differences…
Comment: voomLmFit fitted log-CPM values by Lina ▴ 10
Is the output from fitted(v) in the log2 CPM scale? or CPM scale?
Answer: voomLmFit fitted log-CPM values by Gordon Smyth 52k
Fitted values are obtained from limma MArrayLM objects by ``` fitted(v) ```
Comment: EuroBioC2024 abstract submission is open! by Finnianfly • 0
What specific requirements should be noted when preparing abstracts for presentation formats such as short talks, package demos, or posters…
Votes
Answer: ROAST compare results with complex design
How to account for solvent controls in DESeq2 when comparing follicular vs luteal phase?
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Awards • All
Popular Question to sum31278 • 0
Popular Question to Gordon Smyth 52k
Popular Question to boczniak767 ▴ 740
Popular Question to Young Tae • 0
Popular Question to Robert Castelo ★ 3.4k
Locations • All
The city by the bay, 28 minutes ago
Pittsburgh, United States, 1 hour ago
EMBL Heidelberg, 1 hour ago
San Diego, 3 hours ago
WEHI, Melbourne, Australia, 10 hours ago
Traffic: 882 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6