Showing : scran • reset
9
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4
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5.0k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ▴ 40
8
votes
4
replies
2.2k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 50
7
votes
3
replies
4.7k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
7
votes
5
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1.6k
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 30
7
votes
5
replies
2.4k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
6
votes
1
reply
3.1k
views
Downstream analysis after using mnnCorrect()
scran mnncorrect
updated 6.2 years ago by ★ 28k • written 6.2 years ago by ▴ 210
6
votes
12
replies
3.6k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
5
votes
4
replies
6.0k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 660
5
votes
6
replies
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 20
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.1 years ago by ★ 28k • written 6.1 years ago by • 0
4
votes
3
replies
1.4k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 20 months ago by 65k • written 20 months ago by ▴ 10
4
votes
5
replies
1.7k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.0 years ago by ▴ 150 • written 5.0 years ago by ▴ 50
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 670
4
votes
5
replies
2.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
4
votes
0
replies
3.4k
views
Tutorial: Workflow for low-level analysis of single-cell RNA-seq data
scran scater single cell Tutorial
7.6 years ago Aaron Lun ★ 28k
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
3
votes
7
replies
2.7k
views
Error: could not find function "findMarkers"
scran
6.7 years ago ravi_patel_4 ▴ 10
3
votes
1
reply
1.0k
views
Output lfc for Wilcox-based findMarkers
scran
updated 3.9 years ago by ★ 28k • written 3.9 years ago by ★ 4.0k
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 6.5 years ago by ▴ 90 • written 6.5 years ago by • 0
3
votes
3
replies
1.6k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
3
votes
5
replies
2.1k
views
Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 7.8 years ago by ★ 28k • written 7.8 years ago by ▴ 10
3
votes
3
replies
7.0k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.8 years ago by 25k • written 6.0 years ago by ▴ 10
3
votes
4
replies
1.8k
views
Scran normalization error with computeSumFactors
scran scater
updated 7.2 years ago by ★ 28k • written 7.2 years ago by ▴ 20
3
votes
9
replies
4.1k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.0 years ago by ★ 28k • written 7.0 years ago by ▴ 10
3
votes
2
replies
1.1k
views
Is logFC a log2 fold change or some other base in scran::findMarkers
scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
3
votes
3
replies
1.1k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
22 months ago • updated 20 months ago matthias-doering ▴ 40
3
votes
1
reply
1.1k
views
Normalizing vs RNA content in scRNAseq data
monocle scran
updated 6.8 years ago by ★ 28k • written 6.8 years ago by ▴ 40
3
votes
7
replies
1.9k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
2
votes
2
replies
1.8k
views
[MnnCorrect] Remove batch effects but keep condition effects
single-cell scran mnncorrect rnaseq
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 10
2
votes
3
replies
1.8k
views
multiBatchNorm vs. calculateSumFactors on concatenated dataset
batchelor scran
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
2
votes
6
replies
1.1k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.8 years ago by ★ 28k • written 3.8 years ago by • 0
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.0 years ago by ▴ 760 • written 2.0 years ago by • 0
2
votes
2
replies
2.0k
views
Error in installation of scran
S4Vectors IRanges XVector GenomicRanges scran
updated 5.3 years ago by ★ 28k • written 5.3 years ago by • 0
2
votes
5
replies
3.7k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 20 months ago by ▴ 60 • written 5.2 years ago by ▴ 50
2
votes
5
replies
1.4k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
2
votes
1
reply
1.3k
views
scran: excluding genes with extremely high expression during normalization?
single-cell RNA-seq scran normalization
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
2
votes
2
replies
1.2k
views
scuttle:: librarySizeFactors returning non-finite values
normalizeCounts scran librarySizeFactors scuttle scRNAseq
2.2 years ago • updated 2.1 years ago behr201 • 0
2
votes
2
replies
1.0k
views
normalization for infected homogenious cell populations
normalization single cell scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by • 0
2
votes
1
reply
1.9k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
2
votes
4
replies
3.5k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 2.1 years ago by • 0 • written 5.0 years ago by ▴ 10
2
votes
5
replies
5.8k
views
RNA-Seq Batch correction negative values
rna-seq batch-effect combat scran sva
updated 6.6 years ago by ★ 28k • written 6.6 years ago by ▴ 20
2
votes
2
replies
1.7k
views
loading scran package
scran installation
3.2 years ago TJ • 0
2
votes
3
replies
1.3k
views
Scran functions not found
single-cell scran
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
2
votes
2
replies
992
views
Block weights in scran::pairwiseTTests
scran
2.4 years ago Angelos Armen • 0
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
10 months ago Lluís Revilla Sancho ▴ 730
2
votes
2
replies
1.0k
views
scran: trendVar() / lm.fit() fails in single-cell RNAseq experiment
scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
2
votes
2
replies
5.1k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 10 months ago by ▴ 710 • written 10 months ago by ★ 1.5k
2
votes
3
replies
3.1k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.0 years ago aatsmith • 0
50 results • Page 1 of 1
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Comment: FilterByExpr low counts with small sample size by Gordon Smyth 50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures by Gordon Smyth 50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Comment: Methylation Analysis experiment design using Limma by Gordon Smyth 50k
I don't analyse methylation arrays so cannot advise on specific limma settings for that type of data. Please follow the advice of the methy…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for further guidance! I discussed this issue with psychology doctor who treat Alzheimer patients and they don'…
Comment: Single-Cell Data Simulation from Bulk RNA-seq by wichaidi • 0
Hi - I am wondering what you decided to do. I am currently in a similar condition where I need to create a toy scRNAseq data from bulk.
Votes
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
DESeq2 variance transformation error and plot dispersion Estimate
A: DESeq2 variance transformation error and plot dispersion Estimate
ensembl to hgnc symbols creates duplicates
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