Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
scater
•
reset
0
votes
6
replies
1.4k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 9 days ago by
mhem
• 0 • written 15 days ago by
inzirio
▴ 10
0
votes
3
replies
785
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 12 weeks ago by
ATpoint
★ 3.6k • written 12 weeks ago by
Abbi Edwards
• 0
0
votes
6
replies
606
views
plotHeatmap annotation error
plotHeatmap
scater
5 months ago
Alina
• 0
1
vote
0
replies
829
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
9 months ago
cathalgking
▴ 10
0
votes
1
reply
455
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 10 months ago by
alan.ocallaghan
▴ 120 • written 10 months ago by
cathalgking
▴ 10
1
vote
2
replies
898
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
13 months ago
Guandong Shang
▴ 40
0
votes
4
replies
1.6k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 15 months ago by
Aaron Lun
★ 28k • written 16 months ago by
Guandong Shang
▴ 40
3
votes
2
replies
1.2k
views
FeaturePlot in scater
scater
OSCA
17 months ago
Guandong Shang
▴ 40
5
votes
4
replies
1.3k
views
scater runUMAP
scater
runUMAP
20 months ago
jianhai.zhang
• 0
2
votes
1
reply
862
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 20 months ago by
Basti
▴ 740 • written 20 months ago by
Lucky
• 0
0
votes
6
replies
2.5k
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 21 months ago by
alan.ocallaghan
▴ 120 • written 21 months ago by
tinyimp80
• 0
2
votes
7
replies
1.4k
views
calculateTSNE with large dataset
runTSNE
calculateTSNE
scater
updated 21 months ago by
mikhael.manurung
▴ 270 • written 21 months ago by
alaihd
▴ 10
1
vote
2
replies
750
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
21 months ago
msn
▴ 10
1
vote
2
replies
980
views
More than 3 dimensions in runTSNE
dimensions
scater
runTSNE
2.0 years ago
jianhai.zhang
• 0
3
votes
3
replies
1.4k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.1 years ago
enricoferrero
▴ 660
2
votes
3
replies
963
views
scater::plotHeatmap with swap_rownames gives error
scater
2.1 years ago
enricoferrero
▴ 660
2
votes
2
replies
1.1k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
2.5 years ago
doliv071
• 0
2
votes
3
replies
1.1k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment
scater
updated 2.8 years ago by
alan.ocallaghan
▴ 120 • written 2.8 years ago by
rogerbear
• 0
3
votes
2
replies
1.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
2.8 years ago
camerond
• 0
4
votes
5
replies
1.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
enricoferrero
▴ 660
2
votes
7
replies
2.1k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 2.0 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
p.joshi
▴ 40
0
votes
0
replies
633
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
3.1 years ago
hamza_karakurt
▴ 50
3
votes
3
replies
2.1k
views
What lengths are used to calculate TPM in "scater" package
scater
calculateTPM
RNAseq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
Matan G.
▴ 50
5
votes
5
replies
1.5k
views
Running NMF for single cell
NMF
scater
3.1 years ago
lirongrossmann
▴ 40
0
votes
1
reply
901
views
Change annotation colors plotHeatmap
scater
plotHeatmap
3.2 years ago
simone.avesani22
• 0
5
votes
4
replies
5.4k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
enricoferrero
▴ 660
2
votes
1
reply
928
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
ATpoint
★ 3.6k
0
votes
1
reply
984
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment
sce
scater
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
bharris
• 0
0
votes
4
replies
963
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Jenny Drnevich
★ 2.0k
2
votes
4
replies
1.9k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 2.8 years ago by
1498554536
• 0 • written 3.7 years ago by
Linda
• 0
0
votes
1
reply
828
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
santos22903
• 0
4
votes
1
reply
1.1k
views
could not find function "plotQC" in scater package
scater
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
moldach
▴ 20
2
votes
1
reply
1.6k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
hamza_karakurt
▴ 50
4
votes
4
replies
2.5k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.3k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 670
3
votes
7
replies
1.6k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.3k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 670
0
votes
7
replies
1.8k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
4.4 years ago
Bogdan
▴ 670
0
votes
1
reply
697
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.5 years ago
hamza_karakurt
▴ 50
2
votes
1
reply
1.0k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
kevin.rue
▴ 320
2
votes
4
replies
3.2k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 20 months ago by
Dayme
• 0 • written 4.6 years ago by
kushshah
▴ 10
8
votes
4
replies
1.9k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
hamza_karakurt
▴ 50
2
votes
3
replies
1.3k
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
kushshah
▴ 10
4
votes
5
replies
1.5k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 4.7 years ago by
Vladimir Kiselev
▴ 150 • written 4.7 years ago by
hamza_karakurt
▴ 50
6
votes
3
replies
2.8k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
kushshah
▴ 10
1
vote
2
replies
1.2k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
hamza_karakurt
▴ 50
2
votes
5
replies
1.2k
views
Modularity values of clusters and Differential Expression in scRNA-Seq
scater
scran
igraph
scRNA-Seq
rots
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
hamza_karakurt
▴ 50
2
votes
5
replies
3.3k
views
Adding labels on clusters in a t-SNE plot and changing colors
scran
scater
Rtsne
ggplot2
scRNA-Seq
updated 15 months ago by
jamie.gearing
▴ 60 • written 4.8 years ago by
hamza_karakurt
▴ 50
2
votes
2
replies
1.3k
views
scater error: invalid rownames length
scater
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
lileijie1992
• 0
1
vote
2
replies
941
views
scran/scater Normalized matrix
scran
scater
normalized counts
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Radek
▴ 90
50 results • Page
1 of 1
Recent ...
Replies
Comment: Problem loading HDF5Array in R 4.3.2
by
Mike Smith
★ 6.2k
Great, I'm glad it worked. It's frustrating that the binary doesn't work for you; that shouldn't happen! However I'm not sure how to go a…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
No, I don't. Confirm that `geneList` has the expected format. What is the outcome of `geneList[1:5]`, `str(geneList)` and `class(geneList)…
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
Guido Hooiveld
★ 3.8k
Did you try it yourselves? But the answer is yes.
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Also do you know if the gaphical functions as dotplot, enrichmap and cnetplot works on this generic analysis? still sorry for bothering you
Comment: It's possible to use clusterProfiler without an annotationDBI package
by
nromerov
• 0
Thank you very much for your help iu was really deseperate about this that i wasn't thinking too well yesterday im really gratefull with yo…
Votes
Comment: Problem loading HDF5Array in R 4.3.2
Answer: gseGO input list
Comment: Problem loading HDF5Array in R 4.3.2
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Awards
• All
Popular Question
to
snijesh
▴ 20
Popular Question
to
prathap1708
• 0
Popular Question
to
ary.lech
▴ 10
Scholar
to
Mike Smith
★ 6.2k
Scholar
to
Hervé Pagès
16k
Locations
• All
United States,
3 minutes ago
France,
3 minutes ago
Denmark,
11 minutes ago
Netherlands,
39 minutes ago
France,
44 minutes ago
Traffic: 619 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6