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Showing :
Scater
•
reset
0
votes
0
replies
35
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
15 days ago
cathalgking
• 0
1
vote
2
replies
298
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
3 months ago
Guandong Shang
▴ 40
0
votes
4
replies
468
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 5 months ago by
Aaron Lun
★ 28k • written 6 months ago by
Guandong Shang
▴ 40
3
votes
2
replies
457
views
FeaturePlot in scater
scater
OSCA
7 months ago
Guandong Shang
▴ 40
5
votes
4
replies
631
views
scater runUMAP
scater
runUMAP
9 months ago
jianhai.zhang
• 0
2
votes
1
reply
378
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 9 months ago by
Basti
▴ 530 • written 9 months ago by
Lucky
• 0
0
votes
6
replies
1.5k
views
runPCA error / Error in runSVD(x, k = rank, nu = ifelse(get.pcs, rank, 0), nv = ifelse(get.rotation, : argument "rank" is missing, with no default
scater
updated 11 months ago by
alan.ocallaghan
▴ 120 • written 11 months ago by
tinyimp80
• 0
2
votes
7
replies
689
views
calculateTSNE with large dataset
runTSNE
calculateTSNE
scater
updated 11 months ago by
mikhael.manurung
▴ 270 • written 11 months ago by
alaihd
▴ 10
1
vote
2
replies
422
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
11 months ago
msn
• 0
1
vote
2
replies
585
views
More than 3 dimensions in runTSNE
dimensions
scater
runTSNE
14 months ago
jianhai.zhang
• 0
3
votes
3
replies
797
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
15 months ago
enricoferrero
▴ 650
2
votes
3
replies
573
views
scater::plotHeatmap with swap_rownames gives error
scater
15 months ago
enricoferrero
▴ 650
2
votes
2
replies
649
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
19 months ago
doliv071
• 0
2
votes
3
replies
685
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment
scater
updated 23 months ago by
alan.ocallaghan
▴ 120 • written 23 months ago by
rogerbear
• 0
3
votes
2
replies
947
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
24 months ago • updated 23 months ago
camerond
• 0
4
votes
5
replies
1.1k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 2.0 years ago by
Aaron Lun
★ 28k • written 2.1 years ago by
enricoferrero
▴ 650
2
votes
7
replies
1.2k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 14 months ago by
Aaron Lun
★ 28k • written 2.2 years ago by
p.joshi
▴ 30
0
votes
0
replies
384
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
2.2 years ago
hamza_karakurt
▴ 50
2
votes
3
replies
1.3k
views
What lengths are used to calculate TPM in "scater" package
scater
calculateTPM
RNAseq
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
Matan G.
▴ 40
5
votes
5
replies
987
views
Running NMF for single cell
NMF
scater
2.3 years ago
lirongrossmann
▴ 40
0
votes
1
reply
547
views
Change annotation colors plotHeatmap
scater
plotHeatmap
2.4 years ago
simone.avesani22
• 0
3
votes
4
replies
3.2k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
enricoferrero
▴ 650
2
votes
1
reply
545
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 2.6 years ago by
Aaron Lun
★ 28k • written 2.6 years ago by
ATpoint
★ 2.0k
0
votes
1
reply
552
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment
sce
scater
updated 2.7 years ago by
Aaron Lun
★ 28k • written 2.7 years ago by
bharris
• 0
0
votes
4
replies
565
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 2.8 years ago by
Aaron Lun
★ 28k • written 2.8 years ago by
Jenny Drnevich
★ 2.0k
1
vote
4
replies
1.2k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 24 months ago by
1498554536
• 0 • written 2.9 years ago by
Linda
• 0
0
votes
1
reply
521
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
santos22903
• 0
4
votes
1
reply
781
views
could not find function "plotQC" in scater package
scater
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
moldach
▴ 20
2
votes
1
reply
1.1k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
hamza_karakurt
▴ 50
4
votes
4
replies
1.9k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
Bogdan
▴ 660
4
votes
4
replies
877
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Bogdan
▴ 660
3
votes
7
replies
1.1k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Bogdan
▴ 660
1
vote
4
replies
826
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Bogdan
▴ 660
0
votes
7
replies
933
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
3.6 years ago
Bogdan
▴ 660
0
votes
1
reply
432
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
3.6 years ago
hamza_karakurt
▴ 50
2
votes
1
reply
732
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
kevin.rue
▴ 320
2
votes
4
replies
2.4k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 10 months ago by
Dayme
• 0 • written 3.8 years ago by
kushshah
▴ 10
8
votes
4
replies
1.2k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
hamza_karakurt
▴ 50
2
votes
3
replies
913
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
kushshah
▴ 10
4
votes
5
replies
1.1k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 3.8 years ago by
Vladimir Kiselev
▴ 150 • written 3.8 years ago by
hamza_karakurt
▴ 50
6
votes
3
replies
2.0k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
kushshah
▴ 10
1
vote
2
replies
884
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
hamza_karakurt
▴ 50
2
votes
5
replies
835
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater
scran
igraph
scRNA-Seq
rots
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
hamza_karakurt
▴ 50
2
votes
5
replies
2.4k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran
scater
Rtsne
ggplot2
scRNA-Seq
updated 5 months ago by
jamie.gearing
▴ 60 • written 3.9 years ago by
hamza_karakurt
▴ 50
2
votes
2
replies
936
views
scater error: invalid rownames length
scater
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lileijie1992
• 0
1
vote
2
replies
686
views
scran/scater Normalized matrix
scran
scater
normalized counts
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Radek
▴ 90
7
votes
5
replies
932
views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran
scater
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
heyao
▴ 30
3
votes
3
replies
1.7k
views
Gene ID to Gene Name/Symbol in loom files
Scater
LoomR
SCopeloomR
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Abhishek Singh
▴ 20
0
votes
1
reply
1.7k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 4.1 years ago by
Gordon Smyth
47k • written 4.1 years ago by
hamza_karakurt
▴ 50
1
vote
3
replies
723
views
How to resolve these trendVar() warnings and errors
scater
scran
singlecellexperiment
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Abhishek Singh
▴ 20
50 results • Page
1 of 1
Recent ...
Replies
Comment: Empty ChipQC Report
by
Okan
• 0
Hi, I have the same issue. Have you found any solution or any reason why this is happening?
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Am I understanding correctly that you have 24 RNA-seq libraries in total, 6 from the pooled samples and 18 from regular samples with biolog…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
k.roelfs
• 0
I'm sorry, I know it is kinda confusing... We have 6 pools in total: Phenotype A: T1a, T2, T1b, T1c Phenotype B: T1, T2 Each pool consist…
Comment: edgeR: Usage of estimated dispersion from replicates for pools of the same exper
by
Gordon Smyth
47k
Sorry, I don't understand your experiment. You are reading the edgeR Section on on what to do without replicates, but your experiment appe…
Answer: MA plot
by
Nathalie
• 0
Thank you very much for your help and comments. There is errors in my file. BaseMean is BaseMeanLog2. I don't know how insert a file.
Votes
Comment: How to normalize long-read RNA-seq data for comparison with short-reads
Volcano Plot in R
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: Replicating iDEP parameters in DESeq2; two conditions and an interaction term.
Answer: MA plot
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