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4
votes
1
answer
58
views
1
answer
Usage of doubletCells() function before or after the batch correction?
scran scater scrna-seq doubletcells written 9 days ago by hamza_karakurt • 20 • updated 9 days ago by Aaron Lun • 23k
2
votes
1
answer
81
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1
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Unable to change point size in plotExpression()
scater singlecellexperiment plotexpression plotting written 13 days ago by kushshah • 10 • updated 13 days ago by Aaron Lun • 23k
2
votes
1
answer
67
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1
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ERROR - Size factors should be positive real numbers (using normalize() function)
qc scran scater singlecellexperiment normalize written 15 days ago by kushshah • 10 • updated 15 days ago by Aaron Lun • 23k
4
votes
1
answer
77
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1
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Using SC3 with batch corrected MNN values
scran scater sc3 scrna-seq batch correction written 20 days ago by hamza_karakurt • 20 • updated 20 days ago by Vladimir Kiselev • 150
6
votes
1
answer
140
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1
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Log2(RPKM) counts in Bioconductor
R rpkm expression scater calcaverage written 20 days ago by kushshah • 10 • updated 20 days ago by Aaron Lun • 23k
1
vote
1
answer
110
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1
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Dunn Index for Clusters from scRNA-Seq
clustering scran scater scrna-seq dunn index written 6 weeks ago by hamza_karakurt • 20 • updated 6 weeks ago by Aaron Lun • 23k
2
votes
1
answer
111
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1
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Modularity values of clusters and Differential Expression in scRNA-Seq
igraph scran scater scrna-seq rots written 8 weeks ago by hamza_karakurt • 20 • updated 8 weeks ago by Aaron Lun • 23k
1
vote
1
answer
96
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1
answer
Adding labels on clusters in a t-SNE plot and changing colors
ggplot2 rtsne scran scater scrna-seq written 9 weeks ago by hamza_karakurt • 20 • updated 8 weeks ago by Aaron Lun • 23k
2
votes
1
answer
94
views
1
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scater error: invalid rownames length
scater written 9 weeks ago by lileijie1992 • 0 • updated 9 weeks ago by Aaron Lun • 23k
0
votes
1
answer
101
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1
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scran/scater Normalized matrix
scran normalized counts scater written 3 months ago by Radek • 50 • updated 3 months ago by Aaron Lun • 23k
7
votes
1
answer
150
views
1
answer
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater written 3 months ago by heyao • 30 • updated 3 months ago by Aaron Lun • 23k
2
votes
1
answer
177
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1
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Gene ID to Gene Name/Symbol in loom files
scater loomr scopeloomr written 4 months ago by Abhishek Singh • 20 • updated 4 months ago by Aaron Lun • 23k
0
votes
1
answer
230
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1
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Deconvolution Method in Seurat and convert from SingleCellExperiment
rnaseq scater seurat singlecellexperiment written 4 months ago by hamza_karakurt • 20 • updated 4 months ago by Gordon Smyth ♦ 37k
1
vote
1
answer
140
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1
answer
How to resolve these trendVar() warnings and errors
scran scater singlecellexperiment written 4 months ago by Abhishek Singh • 20 • updated 4 months ago by Aaron Lun • 23k
2
votes
1
answer
156
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1
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Top variable features used by 'runPCA' in scater
pca scater features written 4 months ago by jws • 0 • updated 4 months ago by Aaron Lun • 23k
3
votes
1
answer
160
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1
answer
plotPlatePosition and plate_position
R scater singlecellexperiment written 4 months ago by TJ • 0 • updated 4 months ago by Aaron Lun • 23k
0
votes
1
answer
223
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1
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Problem installing scater
R bioconductor scater biocmanager written 4 months ago by hfberg • 0 • updated 4 months ago by Aaron Lun • 23k
2
votes
1
answer
173
views
1
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Change the number of clusters with scater
clustering scran scater scrnaseq written 5 months ago by shbrief • 10 • updated 5 months ago by Aaron Lun • 23k
1
vote
1
answer
382
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1
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newSCESet and SingleCellExperiment basic differences and TMM Normalization
rnaseq single-cell scater seurat singlecellexperiment written 6 months ago by hamza_karakurt • 20
0
votes
1
answer
354
views
1
answer
Scater package PlotExpression
scater written 8 months ago by mayank.geit89 • 0
0
votes
1
answer
180
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1
answer
RNAseq scater error in plotQC()
scater scrnaseq plotqc written 9 months ago by Vladimir Krasikov • 90 • updated 9 months ago by Aaron Lun • 23k
3
votes
1
answer
979
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1
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rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scran single-cell scater written 11 months ago by MengChun Tseng • 10 • updated 9 months ago by Martin Morgan ♦♦ 23k
0
votes
1
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267
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1
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Converting scater-normalized UMI data to Monocle CellDataSet
monocle scran scater umi written 12 months ago by supremerulersuraj • 0 • updated 12 months ago by Aaron Lun • 23k
5
votes
1
answer
252
views
1
answer
Accessing normalized counts
scater splatter singlecellexperiment written 12 months ago by luke.zappia • 50
0
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2
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1.3k
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2
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Change point size and remove outline in scater's plotPCA
rnaseq single-cell scater written 23 months ago by CodeAway • 30 • updated 12 months ago by angela.ubn • 0
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