Showing : scran • reset
4
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15
replies
4.0k
views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
updated 6.2 years ago by ★ 28k • written 6.2 years ago by • 0
6
votes
12
replies
3.7k
views
Merging RNAseq Datasets of Different Depths
singlecellexperiment scran sequencing depth batch effect scrnaseq
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
3
votes
9
replies
4.2k
views
Why does scran's computeSumFactors produce different size factors for cells with the exact same gene counts?
scran scater drop-seq scrnaseq
updated 7.1 years ago by ★ 28k • written 7.1 years ago by ▴ 10
0
votes
8
replies
2.0k
views
Using Scran with RSEM/DEseq
scran normalization deseq2 rsem edger
7.8 years ago a.guerra • 0
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
3
votes
7
replies
2.8k
views
Error: could not find function "findMarkers"
scran
6.7 years ago ravi_patel_4 ▴ 10
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
4.9 years ago Bogdan ▴ 670
5
votes
6
replies
1.7k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.3 years ago by ★ 28k • written 3.3 years ago by • 0
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.9 years ago by ★ 28k • written 3.9 years ago by • 0
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater scran scrnaseq clustering
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 20
0
votes
6
replies
1.6k
views
scran::trendVar throwing error
scran
6.4 years ago zhalehsafikhani • 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 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 30
2
votes
5
replies
3.8k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
updated 21 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 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 50
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 5.1 years ago by ▴ 150 • written 5.1 years ago by ▴ 50
0
votes
5
replies
2.3k
views
[MnnCorrect] In case of known subpopulations
scran single-cell mnncorrect rnaseq
6.8 years ago Jens Preussner ▴ 30
2
votes
5
replies
5.9k
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
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
7
votes
5
replies
2.5k
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
0
votes
5
replies
3.2k
views
Cannot install Bioconductor v3.9
scran cellassign bioconductor
updated 4.6 years ago by 25k • written 4.6 years ago by ▴ 10
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran simpleSingleCell
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.4 years ago by ★ 28k • written 3.4 years ago by ▴ 660
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
4
votes
4
replies
1.8k
views
Some questions for remove batch effect by using mnnCorrect
batch effect single cells mnnCorrect scran
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 670
3
votes
4
replies
1.9k
views
Scran normalization error with computeSumFactors
scran scater
updated 7.3 years ago by ★ 28k • written 7.3 years ago by ▴ 20
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 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 670
2
votes
4
replies
3.6k
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 5.1 years ago by ▴ 10
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
0
votes
4
replies
1.4k
views
scran's quickCluster error
scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
1
vote
4
replies
1.0k
views
Missing design when using Scran to create a DESeqDataSet
deseq2 Scran
updated 6.6 years ago by ★ 28k • written 6.6 years ago by • 0
8
votes
4
replies
2.3k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 50
9
votes
4
replies
5.1k
views
Removing cell cycle genes in large data set integration
scran cyclone
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
1
vote
3
replies
1.1k
views
Normalizing to multiple spike-in concentrations with scran
scran spike-in
6.2 years ago • updated 6.1 years ago supremerulersuraj • 0
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.1 years ago • updated 8.0 years ago aatsmith • 0
2
votes
3
replies
1.3k
views
Scran functions not found
single-cell scran
updated 6.7 years ago by ★ 28k • written 6.7 years ago by • 0
3
votes
3
replies
2.3k
views
is SCEset fully abandoned in scran?
scran scater splatter normalization
updated 6.6 years ago by ▴ 90 • written 6.6 years ago by • 0
1
vote
3
replies
1.7k
views
scater/scran with TPMs from Salmon - counts?
scater salmon scran
updated 6.3 years ago by ★ 28k • written 6.3 years ago by • 0
3
votes
3
replies
7.1k
views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
updated 5.9 years ago by 25k • written 6.0 years ago by ▴ 10
0
votes
3
replies
984
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 5.8 years ago by ★ 28k • written 5.8 years ago by • 0
1
vote
3
replies
1.1k
views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
1
vote
3
replies
937
views
k argument in buildSNNGraph
scran
updated 4.8 years ago by ★ 28k • written 4.8 years ago by • 0
0
votes
3
replies
974
views
How can doubletCell() scores be converted to single/doublet annotation?
scran doublet
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
7
votes
3
replies
5.0k
views
Downsample or not to downsample?
scrna-seq downsampleBatches scran
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
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
3
votes
3
replies
1.2k
views
RFC: Inconsistent software license for scran & automated license checks
agpl license gpl scran
23 months ago • updated 21 months ago matthias-doering ▴ 40
2
votes
3
replies
1.3k
views
P-value histogram of testLinearModel is not uniform
smart-seq2 scRNAseq scran
11 months ago Lluís Revilla Sancho ▴ 730
4
votes
3
replies
1.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months ago by ▴ 10
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.6 years ago • updated 2.5 years ago enricoferrero ▴ 660
0
votes
3
replies
474
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 4 months ago by ★ 4.1k • written 4 months ago by • 0
50 results • Page 1 of 1
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Answer: Numerical differences in DESeq2 output depending on different design matrix cons by Michael Love 42k
Yes there can be small numerical differences in the estimated quantities because of how the algorithms decide to stop iterating.
Answer: DESeq2- Mysterious interaction suppresses DEGs by Michael Love 42k
Removing samples from one group nevertheless changes the variance estimation (dispersion) for all comparisons. So you could have pushed one…
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by JKim • 0
The 1st model has an interaction term, but the 2nd model doesn't have the interaction term. That makes the difference.
Comment: Ensembl plants at annotationHub? by Daniele • 0
Hi, I'm using Ensembl Plants release 59 with the IWGSC RefSeq v1.1 gene annotation. Thanks a lot for replying so quickly!
Comment: Numerical differences in DESeq2 output depending on different design matrix cons by swbarnes2 ★ 1.4k
If you restrict yourself to, say, genes with a baseMean > 50, are the numerical differences between the two designs significant?
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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