Showing : SCRAN • reset
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Help with the code for "BiocNeighbors::generic_find_knn() function used by scran::quickCluster()
BiocNeighbors generic_find_knn scran quickCluster
8 days ago • updated 7 days ago Arctic • 0
0
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1
reply
479
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SingleR with multiple single cell references
SingleR scran
updated 7 weeks ago by ★ 28k • written 7 weeks ago by ▴ 180
0
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0
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533
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modelGeneVar in MulticoreParam: wrong args for environment subassignment
BiocParallel scran BiocParall
6 months ago Lluís Revilla Sancho ▴ 760
0
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5
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776
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modelGeneVarByPoisson error selecting bandwidth automatically
scran
updated 9 months ago by ▴ 750 • written 9 months ago by ▴ 760
0
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0
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295
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Differential Gene Wrapper for Propotion of Detected
scran
9 months ago Dario Strbenac ★ 1.6k
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4
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789
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
1
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2
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541
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Reproducibility issue with scran together with lapply and BiocParallel
scran BiocParallel bluster
11 months ago ATpoint ★ 4.8k
2
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1
reply
717
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Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 12 months ago by ★ 4.8k • written 12 months ago by ★ 1.6k
0
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3
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1.1k
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scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 14 months ago by ★ 4.8k • written 15 months ago by • 0
1
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ScRNAseq analysis scran :: quickcluster Error
scRNAseq quickcluster scRNA scran
16 months ago ruba-mahmoud • 0
0
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857
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Speeding up large scale scRNAseq analyses in R and improve memory
scran
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
0
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2
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1.6k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
21 months ago Lluís Revilla Sancho ▴ 760
2
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2
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11k
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scran ScoreMarkers throws a warning
scoreMarkers scran
updated 21 months ago by ▴ 750 • written 21 months ago by ★ 1.5k
2
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3
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1.8k
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P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
22 months ago Lluís Revilla Sancho ▴ 760
0
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2
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Scaling and normalization by deconvolution of SMART-Seq 2 data
scran Clustering SingleCell Normalization
2.0 years ago Assa Yeroslaviz ★ 1.5k
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1.1k
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Use scran's normalization by deconvolution for each individual sample or over all samples
scran Normalization scRNA BatchEffect
2.3 years ago r_grau ▴ 10
4
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3
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2.3k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
1
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1
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1.2k
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setting sizeFactors from scran :: caculateSumFactors.
scran DESeq2
updated 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
3
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3
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1.6k
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RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
2.8 years ago • updated 2.7 years ago matthias-doering ▴ 40
2
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1
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1.6k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
2
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2
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scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
3.1 years ago behr201 • 0
1
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2
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.1 years ago msn ▴ 10
2
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2
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1.4k
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Block weights in scran::pairwiseTTests
scran
3.4 years ago Angelos Armen • 0
1
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1
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1.5k
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scran computeSumFactors showing error
scran single cell
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
3
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3
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2.2k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.5 years ago • updated 3.4 years ago enricoferrero ▴ 680
2
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2
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2.5k
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loading scran package
scran installation
4.1 years ago TJ • 0
5
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6
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2.4k
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DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 4.1 years ago by ★ 28k • written 4.2 years ago by • 0
4
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5
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 680
0
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0
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1.1k
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Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.4 years ago hamza_karakurt ▴ 60
1
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1
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1.3k
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scran::computeSumFactors with single-cell ATAC-seq data
scran
updated 4.4 years ago by ★ 28k • written 4.4 years ago by • 0
1
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1
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2.5k
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findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
2
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3
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2.4k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
5
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4
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7.8k
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scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 680
2
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6
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1.6k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
9
votes
4
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6.4k
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Removing cell cycle genes in large data set integration
scran cyclone
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
0
votes
4
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1.8k
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scran's quickCluster error
scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
3
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1
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1.4k
views
Output lfc for Wilcox-based findMarkers
scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ★ 4.8k
7
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5
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3.9k
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Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
7
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3
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7.4k
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Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 40
0
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3
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1.3k
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 10
2
votes
1
reply
2.5k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 60
1
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1
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1.1k
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Stouffer's method weights in scran::pairwiseWilcox
scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by • 0
0
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5
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3.5k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 5.5 years ago by 25k • written 5.5 years ago by ▴ 10
1
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2
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1.7k
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Mitigating cell cycle effect in scRNA-seq using a blocking factor or design matrix
scran
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
2
votes
1
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1.9k
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scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 5.6 years ago by ★ 28k • written 5.6 years ago by • 0
1
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3
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1.3k
views
k argument in buildSNNGraph
scran
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
1
vote
5
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2.1k
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Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
4
votes
4
replies
3.3k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 670
4
votes
4
replies
2.1k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
3
votes
7
replies
2.6k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
50 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
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Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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