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1
vote
1
answer
95
views
1
answer
newSCESet and SingleCellExperiment basic differences and TMM Normalization
rnaseq single-cell scater seurat singlecellexperiment written 5 weeks ago by hamza_karakurt • 0
0
votes
1
answer
193
views
1
answer
Scater package PlotExpression
scater written 3 months ago by mayank.geit89 • 0
0
votes
1
answer
88
views
1
answer
RNAseq scater error in plotQC()
scater scrnaseq plotqc written 3 months ago by Vladimir Krasikov • 90 • updated 3 months ago by Aaron Lun • 21k
3
votes
1
answer
422
views
1
answer
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scran single-cell scater written 6 months ago by MengChun Tseng • 10 • updated 4 months ago by Martin Morgan ♦♦ 22k
0
votes
1
answer
134
views
1
answer
Converting scater-normalized UMI data to Monocle CellDataSet
monocle scran scater umi written 6 months ago by supremerulersuraj • 0 • updated 6 months ago by Aaron Lun • 21k
5
votes
1
answer
137
views
1
answer
Accessing normalized counts
scater splatter singlecellexperiment written 7 months ago by luke.zappia • 50
0
votes
2
answers
947
views
2
answers
Change point size and remove outline in scater's plotPCA
rnaseq single-cell scater written 18 months ago by CodeAway • 30 • updated 7 months ago by angela.ubn • 0
1
vote
1
answer
174
views
1
answer
Inserting "Biotype" into scater SCE objects
R scater sce biotype written 8 months ago by thebadpenny • 0 • updated 8 months ago by Aaron Lun • 21k
4
votes
3
answers
517
views
3
answers
Warning: negative size factors
scran scater singlecellexperiment size factor negative written 8 months ago by Marina V.V. • 0 • updated 8 months ago by Aaron Lun • 21k
1
vote
1
answer
306
views
1
answer
SingleCellExperiment object cannot be used by Scater package?
scater simplesinglecell singlecellexperiment written 9 months ago by Xingyu • 0 • updated 9 months ago by Aaron Lun • 21k
0
votes
1
answer
196
views
1
answer
calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
scater written 9 months ago by Andrew_McDavid • 150 • updated 9 months ago by Aaron Lun • 21k
0
votes
2
answers
511
views
2
answers
error when installing beachmat
scater beachmat written 11 months ago by j.xu3 • 0 • updated 9 months ago by galib36 • 10
1
vote
1
answer
324
views
1
answer
scater/scran with TPMs from Salmon - counts?
salmon scran scater written 10 months ago by nk • 0 • updated 10 months ago by Aaron Lun • 21k
0
votes
0
answers
198
views
0
answers
scater automatically limit gene list size?
scater written 10 months ago by tsofoon • 0
0
votes
1
answer
353
views
1
answer
Scater read10xResults produces a SingleCellExperiment object that contains dots and no longer works with rowSums
scater written 10 months ago by star0044 • 0 • updated 10 months ago by Aaron Lun • 21k
1
vote
2
answers
445
views
2
answers
SC3_estimate_k formatting error?
scater sc3 written 12 months ago by alexandriapinto1 • 10 • updated 11 months ago by Vladimir Kiselev • 130
5
votes
2
answers
897
views
2
answers
Raw count data for SC3 and SingleCellExperiment set problem
scater sc3 singlecellexperiment written 12 months ago by chengyuzou • 10 • updated 12 months ago by Vladimir Kiselev • 130
0
votes
1
answer
342
views
1
answer
Error scatter when creating SingleCellExperiment
scater written 12 months ago by ines.desantiago • 0 • updated 12 months ago by Aaron Lun • 21k
3
votes
1
answer
545
views
1
answer
is SCEset fully abandoned in scran?
normalization scran scater splatter written 12 months ago by wt215 • 0 • updated 12 months ago by davis • 90
0
votes
2
answers
772
views
2
answers
problems when working with SingleCellExperiment object in scater
scater singlecellexperiment written 13 months ago by chriad • 10 • updated 13 months ago by davis • 90
3
votes
1
answer
511
views
1
answer
Error when merging SCESet objects
single-cell scater written 14 months ago by NathL • 0 • updated 14 months ago by Aaron Lun • 21k
1
vote
1
answer
578
views
1
answer
Does SC3 correct counts for gene length?
rna-seq single-cell scater sc3 biclustering written 15 months ago by rmf • 0 • updated 14 months ago by Vladimir Kiselev • 130
1
vote
1
answer
752
views
1
answer
Scater normalizeExprs() batch effect
batch effect scater written 15 months ago by Jenn • 20 • updated 15 months ago by Aaron Lun • 21k
3
votes
2
answers
3.9k
views
2
answers
BiocParallel/scater warning after move to R 3.4.0
biocparallel scater written 18 months ago by nhejazi • 0 • updated 16 months ago by andrew.blake • 30
3
votes
1
answer
751
views
1
answer
Sparse matrices in Bioconductor objects for single-cell analyses
workflows scater simplesinglecell written 17 months ago by sandmann.t • 40 • updated 17 months ago by Aaron Lun • 21k
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