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Scater
•
reset
0
votes
7
replies
1.7k
views
error when installing beachmat
beachmat
scater
updated 6.2 years ago by
galib36
▴ 10 • written 6.4 years ago by
j.xu3
• 0
4
votes
3
replies
1.8k
views
using SC3 and scater for bulk-RNAseq
sc3
scater
scRNAseq
updated 7.1 years ago by
Vladimir Kiselev
▴ 150 • written 7.1 years ago by
Assa Yeroslaviz
★ 1.5k
4
votes
15
replies
3.9k
views
Warning: negative size factors
size factor
negative
scran
singlecellexperiment
scater
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Marina V.V.
• 0
1
vote
8
replies
2.3k
views
SC3_estimate_k formatting error?
sc3
scater
updated 6.4 years ago by
Vladimir Kiselev
▴ 150 • written 6.4 years ago by
alexandriapinto1
▴ 10
4
votes
7
replies
6.3k
views
BiocParallel/scater warning after move to R 3.4.0
biocparallel
scater
updated 6.8 years ago by
andrew.blake
▴ 40 • written 7.0 years ago by
nhejazi
• 0
1
vote
7
replies
6.3k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 6 weeks ago by
Hervé Pagès
16k • written 5 months ago by
inzirio
▴ 10
3
votes
3
replies
319
views
plotUMAP Gene Set Faceted
scater
updated 11 weeks ago by
alan.ocallaghan
▴ 160 • written 11 weeks ago by
Dario Strbenac
★ 1.5k
0
votes
4
replies
4.8k
views
Change point size and remove outline in scater's plotPCA
scater
rnaseq
single-cell
updated 6.0 years ago by
angela.ubn
• 0 • written 6.9 years ago by
CodeAway
▴ 70
1
vote
2
replies
1.4k
views
plotRLE not working in scater
software error
scater
plotRLE
6.9 years ago
ian.oslo
• 0
0
votes
2
replies
3.9k
views
problems when working with SingleCellExperiment object in scater
scater
SingleCellExperiment
updated 6.6 years ago by
davis
▴ 90 • written 6.6 years ago by
chriad
▴ 10
4
votes
5
replies
2.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
enricoferrero
▴ 660
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
Aaron Lun
★ 28k • written 3.7 years ago by
enricoferrero
▴ 660
0
votes
16
replies
2.4k
views
How does newSCESet calculate expression matrix
scater
updated 6.9 years ago by
davis
▴ 90 • written 6.9 years ago by
siajunren
• 0
5
votes
2
replies
5.8k
views
Raw count data for SC3 and SingleCellExperiment set problem
singlecellexperiment
sc3
scater
updated 6.4 years ago by
Vladimir Kiselev
▴ 150 • written 6.4 years ago by
chengyuzou
▴ 10
0
votes
1
reply
665
views
calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
scater
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Andrew_McDavid
▴ 270
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Xingyu
• 0
1
vote
2
replies
868
views
Inserting "Biotype" into scater SCE objects
scater
sce
biotype
R
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
thebadpenny
• 0
5
votes
2
replies
1.6k
views
Accessing normalized counts
splatter
singlecellexperiment
scater
6.0 years ago
luke.zappia
▴ 50
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
Aaron Lun
★ 28k • written 6.0 years ago by
supremerulersuraj
• 0
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
Martin Morgan
25k • written 6.0 years ago by
MengChun Tseng
▴ 10
0
votes
1
reply
982
views
RNAseq scater error in plotQC()
scater
plotQC
scRNAseq
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
Vladimir Krasikov
▴ 90
0
votes
6
replies
1.6k
views
Scater package PlotExpression
scater
5.7 years ago
mayank.geit89
• 0
1
vote
5
replies
2.5k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment
single-cell
rnaseq
seurat
scater
5.5 years ago
hamza_karakurt
▴ 50
2
votes
6
replies
1.7k
views
Change the number of clusters with scater
scater
scran
scrnaseq
clustering
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
shbrief
▴ 20
0
votes
2
replies
2.8k
views
Problem installing scater
scater
R
biocmanager
bioconductor
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
hfberg
• 0
3
votes
5
replies
1.2k
views
plotPlatePosition and plate_position
scater
R
singlecellexperiment
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
TJ
• 0
2
votes
1
reply
1.2k
views
Top variable features used by 'runPCA' in scater
scater
pca
features
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
jws
• 0
1
vote
3
replies
1.1k
views
How to resolve these trendVar() warnings and errors
scater
scran
singlecellexperiment
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Abhishek Singh
▴ 20
0
votes
1
reply
2.4k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 5.3 years ago by
Gordon Smyth
50k • written 5.3 years ago by
hamza_karakurt
▴ 50
3
votes
3
replies
2.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater
LoomR
SCopeloomR
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Abhishek Singh
▴ 20
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
Aaron Lun
★ 28k • written 5.3 years ago by
heyao
▴ 30
1
vote
2
replies
1.1k
views
scran/scater Normalized matrix
scran
scater
normalized counts
updated 5.3 years ago by
Aaron Lun
★ 28k • written 5.3 years ago by
Radek
▴ 90
2
votes
2
replies
1.4k
views
scater error: invalid rownames length
scater
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
lileijie1992
• 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
jamie.gearing
▴ 60 • written 5.2 years ago by
hamza_karakurt
▴ 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
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
7
votes
3
replies
3.2k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
kushshah
▴ 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
Vladimir Kiselev
▴ 150 • written 5.0 years ago by
hamza_karakurt
▴ 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
Dayme
• 0 • written 5.0 years ago by
kushshah
▴ 10
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
kushshah
▴ 10
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
Aaron Lun
★ 28k • written 5.0 years ago by
hamza_karakurt
▴ 50
2
votes
1
reply
1.1k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
kevin.rue
▴ 350
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
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
3
votes
7
replies
1.9k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
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
Aaron Lun
★ 28k • written 4.7 years ago by
Bogdan
▴ 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
Aaron Lun
★ 28k • written 4.5 years ago by
hamza_karakurt
▴ 50
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
moldach
▴ 20
0
votes
1
reply
980
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
santos22903
• 0
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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…
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Hi Gordon, thank you so much for further guidance! I discussed this issue with doctor know about Alzheimer and they don't expect significan…
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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.
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• 0
Hi, Thank you very much for your answer. It's true that I only used 6 samples for this analysis, which is consistent with your explanation…
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• 0
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