Showing : scater • reset
2
Votes
5
Replies
101
Views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
10 days ago enricoferrero • 570 • updated 10 days ago Aaron Lun ♦ 26k
2
Votes
2
Replies
85
Views
How to run runNMF in parallel?
scater single SingleCellExperiment
10 weeks ago p.joshi • 20
0
Votes
0
Replies
34
Views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
10 weeks ago hamza_karakurt • 50
2
Votes
3
Replies
224
Views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
3 months ago Matan G. • 30 • updated 12 weeks ago Aaron Lun ♦ 26k
5
Votes
5
Replies
156
Views
Running NMF for single cell
NMF scater
3 months ago lirongrossmann • 30
0
Votes
1
Reply
113
Views
Change annotation colors plotHeatmap
scater plotHeatmap
4 months ago simone.avesani22 • 0
3
Votes
4
Replies
255
Views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
5 months ago enricoferrero • 570 • updated 5 months ago Aaron Lun ♦ 26k
2
Votes
1
Reply
75
Views
Scaling option in fastMNN
fastmnn scater batchelor
7 months ago ATpoint • 390 • updated 7 months ago Aaron Lun ♦ 26k
0
Votes
1
Reply
56
Views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
8 months ago bharris • 0 • updated 8 months ago Aaron Lun ♦ 26k
0
Votes
4
Replies
81
Views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
9 months ago Jenny Drnevich ♦ 2.0k • updated 9 months ago Aaron Lun ♦ 26k
0
Votes
2
Replies
92
Views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
10 months ago Linda • 0 • updated 10 months ago Aaron Lun ♦ 26k
0
Votes
1
Reply
205
Views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
13 months ago santos22903 • 0 • updated 13 months ago Aaron Lun ♦ 26k
4
Votes
1
Reply
303
Views
could not find function "plotQC" in scater package
scater
15 months ago moldach • 20 • updated 15 months ago Aaron Lun ♦ 26k
2
Votes
1
Reply
196
Views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
15 months ago hamza_karakurt • 50 • updated 15 months ago Aaron Lun ♦ 26k
4
Votes
4
Replies
708
Views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
18 months ago Bogdan • 610 • updated 18 months ago Aaron Lun ♦ 26k
4
Votes
4
Replies
326
Views
scRNA-seq : Classification of cell cycle phase
scater scran
18 months ago Bogdan • 610 • updated 18 months ago Aaron Lun ♦ 26k
3
Votes
7
Replies
399
Views
scRNA-seq : runPCA() and denoisePCA()
scater scran
18 months ago Bogdan • 610 • updated 18 months ago Aaron Lun ♦ 26k
1
Vote
4
Replies
227
Views
number of cell clusters in scRNA-seq
scran scater sc3
19 months ago Bogdan • 610 • updated 19 months ago Aaron Lun ♦ 26k
0
Votes
7
Replies
240
Views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
19 months ago Bogdan • 610
0
Votes
1
Reply
155
Views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
19 months ago hamza_karakurt • 50
2
Votes
1
Reply
299
Views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
20 months ago kevin.rue • 300 • updated 20 months ago Aaron Lun ♦ 26k
2
Votes
3
Replies
959
Views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
21 months ago • updated 20 months ago kushshah • 10
4
Votes
4
Replies
343
Views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
21 months ago hamza_karakurt • 50 • updated 21 months ago Aaron Lun ♦ 26k
2
Votes
3
Replies
295
Views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
21 months ago kushshah • 10 • updated 21 months ago Aaron Lun ♦ 26k
4
Votes
5
Replies
411
Views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
21 months ago hamza_karakurt • 50 • updated 21 months ago Vladimir Kiselev • 150
6
Votes
3
Replies
543
Views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
21 months ago kushshah • 10 • updated 21 months ago Aaron Lun ♦ 26k
1
Vote
2
Replies
369
Views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq clustering scater scran dunn index
22 months ago hamza_karakurt • 50 • updated 22 months ago Aaron Lun ♦ 26k
2
Votes
5
Replies
311
Views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater scran igraph scRNA-Seq rots
23 months ago hamza_karakurt • 50 • updated 23 months ago Aaron Lun ♦ 26k
1
Vote
2
Replies
809
Views
Adding labels on clusters in a t-SNE plot and changing colors
scran scater Rtsne ggplot2 scRNA-Seq
23 months ago hamza_karakurt • 50 • updated 23 months ago Aaron Lun ♦ 26k
2
Votes
2
Replies
359
Views
scater error: invalid rownames length
scater
23 months ago lileijie1992 • 0 • updated 23 months ago Aaron Lun ♦ 26k
0
Votes
2
Replies
260
Views
scran/scater Normalized matrix
scran scater normalized counts
2.0 years ago Radek • 70 • updated 2.0 years ago Aaron Lun ♦ 26k
7
Votes
5
Replies
383
Views
scran: Are the log counts expression comparable among different genes within a sample/cell ?
scran scater
2.1 years ago heyao • 30 • updated 2.1 years ago Aaron Lun ♦ 26k
2
Votes
3
Replies
627
Views
Gene ID to Gene Name/Symbol in loom files
Scater LoomR SCopeloomR
2.1 years ago Abhishek Singh • 20 • updated 2.1 years ago Aaron Lun ♦ 26k
0
Votes
1
Reply
789
Views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater seurat singlecellexperiment rnaseq
2.1 years ago hamza_karakurt • 50 • updated 2.1 years ago Gordon Smyth 41k
1
Vote
3
Replies
334
Views
How to resolve these trendVar() warnings and errors
scater scran singlecellexperiment
2.1 years ago Abhishek Singh • 20 • updated 2.1 years ago Aaron Lun ♦ 26k
2
Votes
1
Reply
354
Views
Top variable features used by 'runPCA' in scater
scater pca features
2.1 years ago jws • 0 • updated 2.1 years ago Aaron Lun ♦ 26k
3
Votes
5
Replies
359
Views
plotPlatePosition and plate_position
scater R singlecellexperiment
2.1 years ago TJ • 0 • updated 2.1 years ago Aaron Lun ♦ 26k
0
Votes
2
Replies
674
Views
Problem installing scater
scater R biocmanager bioconductor
2.1 years ago hfberg • 0 • updated 2.1 years ago Aaron Lun ♦ 26k
2
Votes
6
Replies
409
Views
Change the number of clusters with scater
scater scran scrnaseq clustering
2.2 years ago shbrief • 10 • updated 2.2 years ago Aaron Lun ♦ 26k
1
Vote
5
Replies
925
Views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment single-cell rnaseq seurat scater
2.3 years ago hamza_karakurt • 50
0
Votes
6
Replies
603
Views
Scater package PlotExpression
scater
2.5 years ago • updated 2.4 years ago mayank.geit89 • 0
0
Votes
1
Reply
349
Views
RNAseq scater error in plotQC()
scater plotQC scRNAseq
2.5 years ago Vladimir Krasikov • 90 • updated 2.5 years ago Aaron Lun ♦ 26k
3
Votes
3
Replies
3.3k
Views
rowSums() rowMeans() don't work on sparse matrix "dgCMatrix"
scater scran single-cell
2.7 years ago MengChun Tseng • 10 • updated 2.6 years ago Martin Morgan 25k
0
Votes
1
Reply
520
Views
Converting scater-normalized UMI data to Monocle CellDataSet
scater scran umi monocle
2.7 years ago supremerulersuraj • 0 • updated 2.7 years ago Aaron Lun ♦ 26k
5
Votes
2
Replies
391
Views
Accessing normalized counts
splatter singlecellexperiment scater
2.8 years ago luke.zappia • 50
0
Votes
4
Replies
2.0k
Views
Change point size and remove outline in scater's plotPCA
scater rnaseq single-cell
3.7 years ago CodeAway • 60 • updated 2.8 years ago angela.ubn • 0
1
Vote
2
Replies
355
Views
Inserting "Biotype" into scater SCE objects
scater sce biotype R
2.9 years ago thebadpenny • 0 • updated 2.9 years ago Aaron Lun ♦ 26k
4
Votes
15
Replies
1.7k
Views
Warning: negative size factors
size factor negative scran singlecellexperiment scater
2.9 years ago Marina V.V. • 0 • updated 2.9 years ago Aaron Lun ♦ 26k
1
Vote
2
Replies
790
Views
SingleCellExperiment object cannot be used by Scater package?
scater singlecellexperiment simplesinglecell
2.9 years ago Xingyu • 0 • updated 2.9 years ago Aaron Lun ♦ 26k
0
Votes
1
Reply
378
Views
calculateQCmetrics doesn't accept `numeric` `feature_controls` in scater 1.6.2
scater
3.0 years ago Andrew_McDavid • 260 • updated 3.0 years ago Aaron Lun ♦ 26k
74 results • Page 1 of 2
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Replies
Comment: How to use EnrichGo of Cluster Profiler by Lluís Revilla Sancho • 610
Could you share what is the output of `head(gene)`?
Comment: DESeq2 Error: ncol(countData) == nrow(colData) is not TRUE by Pedram • 0
Hello Michael I could not make the same matrix although I did what you said
Comment: Replace a specific nucleotide sequence, at a specific position, with another in by Konstantinos Yeles • 40
Hello @Benjamin-24571 for your example, I can suggest you this code: Read <- c("1","2","3","4") Sequences <- c("ACACCCACG", "AA…
Comment: CHIP Seq Analysis by DiffBind Package by shrinka.genetics • 0
Hello Thanks for your reply. I changed my file format and now it ran. It gave one plot also. All file s are in same directory. No…
Answer: Installing Bioconductor packages in Docker by Konstantinos Yeles • 40
Hello, @adklts-21974 My way to do the installation of packages in a docker is like this: FROM bioconductor/bioconductor_docker…
Votes
A: Interpreting the results from lfcShrink() with apeglm in DESeq2
A: single-cells RNA-seq analysis by MAST with unbalanced group size
single-cells RNA-seq analysis by MAST with unbalanced group size
A: single-cells RNA-seq analysis by MAST with unbalanced group size
A: DESeq2 1.20.0 lfcshrink function
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