Showing : Scran • reset
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
5
votes
4
replies
5.9k
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
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
5.1k
views
scran ScoreMarkers throws a warning
scoreMarkers scran
updated 10 months ago by ▴ 700 • written 10 months ago by ★ 1.5k
9
votes
4
replies
4.9k
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
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
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
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
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
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
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
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
0
votes
5
replies
3.1k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.5 years ago by 25k • written 4.5 years ago by ▴ 10
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
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
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
3
votes
7
replies
2.7k
views
Error: could not find function "findMarkers"
scran
6.7 years ago ravi_patel_4 ▴ 10
7
votes
5
replies
2.4k
views
Optimal cluster number identification using buildSNNgraph and igraph clusters
scran gap statistics single cell clustering
updated 3.9 years ago by ★ 28k • written 4.0 years ago by ▴ 40
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
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
0
votes
5
replies
2.2k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
6.7 years ago Jens Preussner ▴ 30
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
1
vote
2
replies
2.2k
views
keep getting this error "number of rows is not the same across batches" even though my 2 matrices have the same row number
mnncorrect batch effect scran
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
0
votes
7
replies
2.1k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.8 years ago Bogdan ▴ 670
3
votes
5
replies
2.1k
views
Using Scran normalization with in edgeR
edger estimatedisp scran sizefactors
updated 7.7 years ago by ★ 28k • written 7.7 years ago by ▴ 10
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
0
votes
8
replies
2.0k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
7.7 years ago a.guerra • 0
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
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
1
vote
1
reply
1.8k
views
findMarkers() {scran} doesn't really find markers
findMarkers scran
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
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
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
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
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
2
replies
1.7k
views
loading scran package
scran installation
3.2 years ago TJ • 0
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
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
3
votes
3
replies
1.6k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
7
votes
5
replies
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
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
2
replies
1.5k
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
0
votes
6
replies
1.5k
views
scran::trendVar throwing error
scran
6.4 years ago zhalehsafikhani • 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
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
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
0
votes
1
reply
1.4k
views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
updated 6.0 years ago by ★ 28k • written 6.0 years ago by • 0
1
vote
2
replies
1.4k
views
SCRAN - Question: Error when calling cosineNorm through fastMNN
SCRAN fastMNN mnnCorrect
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
vote
1
reply
1.4k
views
Adjust number of clusters with scran/buildSNNGraph
scran buildsnngraph cluster_walktrap single-cell
updated 5.7 years ago by ★ 28k • written 5.7 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Comment: DEG with low counts by Rajat • 0
Dear Dr. Michael Thanks for you quick reply. I appreciate it. Attached is the plotcounts for one gene. I am experiencing like this in oth…
Comment: Light difference when using coef vs omit a group when compare 3 groups. by Chris • 0
Hi Gordon, thank you so much for your guide! I check my data as you said there is no difference in my data. This is the MDS plot at genes l…
Comment: How to correct for known and surrogate variables in DESeq2? by Michael Love 41k
To question 3: if you model technical variation using only ~group vs ~1, then it will be correlated with known technical variables, which y…
Answer: flowStats Search Error by shepherl 3.8k
We are aware of an issue with bioconductor.org search and are investigating. We apologize for an inconvenience this is causing.
Comment: How to correct for known and surrogate variables in DESeq2? by nhaus ▴ 30
Hey Crystal, did you end up getting advice? I am facing the exact same questions that you are having right now. Would be very grateful if y…
Votes
Answer: Light difference when using coef vs omit a group when compare 3 groups.
C: Add new columns to DESeqResults from text file by matching rownames.
Answer: geneList error in clusterprofiler
Comment: Memory errors using read.bismark?
Comment: Not fully paired differential gene expression analysis
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