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
2
votes
1
reply
238
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 6 weeks ago by
ATpoint
★ 4.1k • written 6 weeks ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
404
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 6 weeks ago by
alan.ocallaghan
▴ 160 • written 6 weeks ago by
Najla Abassi
• 0
3
votes
3
replies
375
views
plotUMAP Gene Set Faceted
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
249
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 3 months ago by
alan.ocallaghan
▴ 160 • written 3 months ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
6.6k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 9 weeks ago by
Hervé Pagès
16k • written 5 months ago by
inzirio
▴ 10
0
votes
3
replies
1.1k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 8 months ago by
ATpoint
★ 4.1k • written 8 months ago by
Abbi Edwards
• 0
0
votes
6
replies
875
views
plotHeatmap annotation error
plotHeatmap
scater
10 months ago
Alina
• 0
1
vote
0
replies
1.3k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
15 months ago
cathalgking
▴ 10
0
votes
1
reply
660
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 15 months ago by
alan.ocallaghan
▴ 160 • written 16 months ago by
cathalgking
▴ 10
1
vote
2
replies
1.1k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
19 months ago
Guandong Shang
▴ 40
0
votes
4
replies
2.0k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 21 months ago by
Aaron Lun
★ 28k • written 21 months ago by
Guandong Shang
▴ 40
3
votes
2
replies
1.7k
views
FeaturePlot in scater
scater
OSCA
22 months ago
Guandong Shang
▴ 40
5
votes
4
replies
1.6k
views
scater runUMAP
scater
runUMAP
2.1 years ago
jianhai.zhang
• 0
2
votes
1
reply
1.1k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 2.1 years ago by
Basti
▴ 780 • written 2.1 years ago by
Lucky
• 0
2
votes
7
replies
1.7k
views
calculateTSNE with large dataset
runTSNE
calculateTSNE
scater
updated 2.2 years ago by
mikhael.manurung
▴ 270 • written 2.2 years ago by
alaihd
▴ 10
1
vote
2
replies
927
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.2 years ago
msn
▴ 10
0
votes
6
replies
2.9k
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 2.2 years ago by
alan.ocallaghan
▴ 160 • written 2.2 years ago by
tinyimp80
• 0
1
vote
2
replies
1.1k
views
More than 3 dimensions in runTSNE
dimensions
scater
runTSNE
2.5 years ago
jianhai.zhang
• 0
3
votes
3
replies
1.7k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
2.5 years ago
enricoferrero
▴ 660
2
votes
3
replies
1.2k
views
scater::plotHeatmap with swap_rownames gives error
scater
2.5 years ago
enricoferrero
▴ 660
2
votes
2
replies
1.3k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
2.9 years ago
doliv071
• 0
2
votes
3
replies
1.3k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment
scater
updated 3.2 years ago by
alan.ocallaghan
▴ 160 • written 3.2 years ago by
rogerbear
• 0
3
votes
2
replies
2.2k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
3.3 years ago • updated 3.2 years ago
camerond
• 0
4
votes
5
replies
2.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
enricoferrero
▴ 660
2
votes
7
replies
2.6k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 2.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
p.joshi
▴ 40
0
votes
0
replies
771
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
3.5 years ago
hamza_karakurt
▴ 50
3
votes
3
replies
2.4k
views
What lengths are used to calculate TPM in "scater" package
scater
calculateTPM
RNAseq
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
Matan G.
▴ 60
5
votes
5
replies
1.7k
views
Running NMF for single cell
NMF
scater
3.6 years ago
lirongrossmann
▴ 40
0
votes
1
reply
1.0k
views
Change annotation colors plotHeatmap
scater
plotHeatmap
3.6 years ago
simone.avesani22
• 0
5
votes
4
replies
6.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
enricoferrero
▴ 660
2
votes
1
reply
1.1k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
ATpoint
★ 4.1k
0
votes
1
reply
1.2k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment
sce
scater
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
bharris
• 0
0
votes
4
replies
1.2k
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
Jenny Drnevich
★ 2.0k
2
votes
4
replies
2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 3.3 years ago by
1498554536
• 0 • written 4.1 years ago by
Linda
• 0
0
votes
1
reply
1.0k
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
santos22903
• 0
4
votes
1
reply
1.2k
views
could not find function "plotQC" in scater package
scater
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
moldach
▴ 20
2
votes
1
reply
2.0k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
hamza_karakurt
▴ 50
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
3
votes
7
replies
2.0k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.5k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.5k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.2k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
4.9 years ago
Bogdan
▴ 670
0
votes
1
reply
837
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.9 years ago
hamza_karakurt
▴ 50
2
votes
1
reply
1.2k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
kevin.rue
▴ 350
8
votes
4
replies
2.3k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
hamza_karakurt
▴ 50
2
votes
3
replies
1.6k
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
kushshah
▴ 10
2
votes
4
replies
3.6k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 2.1 years ago by
Dayme
• 0 • written 5.1 years ago by
kushshah
▴ 10
4
votes
5
replies
1.8k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.1 years ago by
Vladimir Kiselev
▴ 150 • written 5.1 years ago by
hamza_karakurt
▴ 50
7
votes
3
replies
3.3k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
kushshah
▴ 10
1
vote
2
replies
1.4k
views
Dunn Index for Clusters from scRNA-Seq
scRNA-Seq
clustering
scater
scran
dunn index
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 50
50 results • Page
1 of 1
Recent ...
Replies
Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
by
Hervé Pagès
16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea()
by
James W. MacDonald
65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea()
by
Chris
• 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
Votes
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
Answer: Trim/Filter out-of-bounds GRanges
Comment: Help with running egsea()
Answer: How to save the DEXSeq results
Awards
• All
Scholar
to
Michael Love
41k
Popular Question
to
Malcolm Cook
★ 1.6k
Teacher
to
Gordon Smyth
50k
Popular Question
to
priyanka.m
• 0
Popular Question
to
Vincent J. Carey, Jr.
6.7k
Locations
• All
WEHI, Melbourne, Australia,
25 minutes ago
France,
27 minutes ago
India,
1 hour ago
The city by the bay,
1 hour ago
United States,
1 hour ago
Traffic: 565 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