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3
votes
1
answer
102
views
1
answer
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edger scran scater simplesinglecell written 27 days ago by Bogdan • 560 • updated 26 days ago by Aaron Lun • 24k
4
votes
1
answer
144
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1
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scRNA-seq : Classification of cell cycle phase
scran scater written 7 weeks ago by Bogdan • 560 • updated 7 weeks ago by Aaron Lun • 24k
3
votes
1
answer
176
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1
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scRNA-seq : runPCA() and denoisePCA()
scran scater written 7 weeks ago by Bogdan • 560 • updated 7 weeks ago by Aaron Lun • 24k
1
vote
1
answer
111
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1
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number of cell clusters in scRNA-seq
scran scater sc3 written 7 weeks ago by Bogdan • 560 • updated 7 weeks ago by Aaron Lun • 24k
0
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1
answer
122
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1
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differential expression between clusters (in distinct "treatments") in scRNAseq
limma scran scde scater sc3 written 8 weeks ago by Bogdan • 560
0
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0
answers
76
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0
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emptyDrops result is full NAs
scran scater dropletutils scrna-seq written 9 weeks ago by hamza_karakurt • 30
2
votes
1
answer
125
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1
answer
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater delayedarray biocsingular written 12 weeks ago by kevin.rue • 220 • updated 12 weeks ago by Aaron Lun • 24k
2
votes
1
answer
246
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1
answer
ERROR - Size factors should be positive real numbers (using normalize() function)
qc scran scater singlecellexperiment normalize written 4 months ago by kushshah • 10
4
votes
1
answer
160
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1
answer
Usage of doubletCells() function before or after the batch correction?
scran scater scrna-seq doubletcells written 4 months ago by hamza_karakurt • 30 • updated 4 months ago by Aaron Lun • 24k
2
votes
1
answer
143
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1
answer
Unable to change point size in plotExpression()
scater singlecellexperiment plotexpression plotting written 4 months ago by kushshah • 10 • updated 4 months ago by Aaron Lun • 24k
4
votes
1
answer
186
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1
answer
Using SC3 with batch corrected MNN values
scran scater sc3 scrna-seq batch correction written 4 months ago by hamza_karakurt • 30 • updated 4 months ago by Vladimir Kiselev • 150
6
votes
1
answer
235
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1
answer
Log2(RPKM) counts in Bioconductor
R rpkm expression scater calcaverage written 4 months ago by kushshah • 10 • updated 4 months ago by Aaron Lun • 24k
1
vote
1
answer
197
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1
answer
Dunn Index for Clusters from scRNA-Seq
clustering scran scater scrna-seq dunn index written 5 months ago by hamza_karakurt • 30 • updated 5 months ago by Aaron Lun • 24k
2
votes
1
answer
190
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1
answer
Modularity values of clusters and Differential Expression in scRNA-Seq
igraph scran scater scrna-seq rots written 5 months ago by hamza_karakurt • 30 • updated 5 months ago by Aaron Lun • 24k
1
vote
1
answer
191
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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 5 months ago by hamza_karakurt • 30 • updated 5 months ago by Aaron Lun • 24k
2
votes
1
answer
193
views
1
answer
scater error: invalid rownames length
scater written 5 months ago by lileijie1992 • 0 • updated 5 months ago by Aaron Lun • 24k
0
votes
1
answer
158
views
1
answer
scran/scater Normalized matrix
scran normalized counts scater written 7 months ago by Radek • 60 • updated 7 months ago by Aaron Lun • 24k
7
votes
1
answer
262
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1
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scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater written 7 months ago by heyao • 30 • updated 7 months ago by Aaron Lun • 24k
2
votes
1
answer
296
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1
answer
Gene ID to Gene Name/Symbol in loom files
scater loomr scopeloomr written 7 months ago by Abhishek Singh • 20 • updated 7 months ago by Aaron Lun • 24k
0
votes
1
answer
365
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1
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Deconvolution Method in Seurat and convert from SingleCellExperiment
rnaseq scater seurat singlecellexperiment written 8 months ago by hamza_karakurt • 30 • updated 8 months ago by Gordon Smyth ♦ 38k
1
vote
1
answer
213
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1
answer
How to resolve these trendVar() warnings and errors
scran scater singlecellexperiment written 8 months ago by Abhishek Singh • 20 • updated 8 months ago by Aaron Lun • 24k
2
votes
1
answer
217
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1
answer
Top variable features used by 'runPCA' in scater
pca scater features written 8 months ago by jws • 0 • updated 8 months ago by Aaron Lun • 24k
3
votes
1
answer
232
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1
answer
plotPlatePosition and plate_position
R scater singlecellexperiment written 8 months ago by TJ • 0 • updated 8 months ago by Aaron Lun • 24k
0
votes
1
answer
327
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1
answer
Problem installing scater
R bioconductor scater biocmanager written 8 months ago by hfberg • 0 • updated 8 months ago by Aaron Lun • 24k
2
votes
1
answer
249
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1
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Change the number of clusters with scater
clustering scran scater scrnaseq written 9 months ago by shbrief • 10 • updated 9 months ago by Aaron Lun • 24k
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