Showing : scran • reset
4
votes
15
replies
3.9k
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
3.6k
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
4.1k
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
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
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
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
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
1.6k
views
DE Analysis on Scran-Normalized Counts
DifferentialExpression scRNAseq scran
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
2
votes
6
replies
1.2k
views
Why is an averaged reference used in DESeq2 normalisation?
deseq2 scran batchelor
updated 3.8 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 5.3 years ago by ★ 28k • written 5.3 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 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 5.2 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
5.8k
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
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 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
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
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
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
1.8k
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 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 660
0
votes
4
replies
1.3k
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 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 50
9
votes
4
replies
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
1
vote
3
replies
1.0k
views
Normalizing to multiple spike-in concentrations with scran
scran spike-in
6.1 years ago • updated 6.0 years ago supremerulersuraj • 0
2
votes
3
replies
3.2k
views
scran: question on minimum cluster size for computeSumFactors()
scran single cell normalization clustering
8.0 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 6.5 years ago by ▴ 90 • written 6.5 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 5.8 years ago by 25k • written 6.0 years ago by ▴ 10
0
votes
3
replies
976
views
Error of makeTechTrend() of Scran
scran single-cell seq.default
updated 5.7 years ago by ★ 28k • written 5.7 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
924
views
k argument in buildSNNGraph
scran
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
0
votes
3
replies
961
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
4.9k
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
22 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 • updated 10 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
2.5 years ago enricoferrero ▴ 660
0
votes
3
replies
432
views
scran package: quickCluster and calculateSumFactors parallelization
BiocParallel scran
updated 3 months ago by ★ 4.1k • written 3 months ago by • 0
50 results • Page 1 of 1
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Comment: Timecourse RNASeq analysis by Aurora • 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
But.. How to run a temporal assay?
Comment: Deseq2 and Normalization of RNA sequencing data by kcarey • 0
Noise in terms of expression...to make sure that the information reported is not due to artifacts and actually expression. When I had FPKM …
Answer: NEED FOR NESSASORY HELP by Gordon Smyth 50k
Is this quesion related to your earlier question? https://support.bioconductor.org/p/9157127/ If you've already done an edgeR analysis, yo…
Answer: Gene-by-sample covariates in limma by Gordon Smyth 50k
Your first method would be valid if, instead of taking ratios, you instead used the differences between the log-transformed 13C and 12C int…
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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