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
4
replies
626
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression
scran
scater
SingleCellExperiment
edgeR
6 months ago
vohara4
• 0
3
votes
3
replies
1.4k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater
runPCA
updated 9 months ago by
alan.ocallaghan
▴ 160 • written 9 months ago by
Najla Abassi
• 0
2
votes
1
reply
565
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran
bluster
scater
scuttle
updated 9 months ago by
ATpoint
★ 4.6k • written 9 months ago by
Dario Strbenac
★ 1.5k
3
votes
3
replies
1.2k
views
plotUMAP Gene Set Faceted
scater
updated 10 months ago by
alan.ocallaghan
▴ 160 • written 10 months ago by
Dario Strbenac
★ 1.5k
1
vote
1
reply
567
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 10 months ago by
alan.ocallaghan
▴ 160 • written 11 months ago by
Dario Strbenac
★ 1.5k
1
vote
7
replies
8.6k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP
scater
Matrix
updated 9 months ago by
Hervé Pagès
16k • written 13 months ago by
inzirio
▴ 10
0
votes
3
replies
1.6k
views
Is logNormCounts log2 normalised counts as default?
scuttle
scater
updated 15 months ago by
ATpoint
★ 4.6k • written 15 months ago by
Abbi Edwards
• 0
0
votes
6
replies
1.2k
views
plotHeatmap annotation error
plotHeatmap
scater
18 months ago
Alina
• 0
1
vote
0
replies
1.9k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
22 months ago
cathalgking
▴ 10
0
votes
1
reply
949
views
cell_count column in SpatialExperiment Object
scuttle
scater
SpatialExperiment
updated 23 months ago by
alan.ocallaghan
▴ 160 • written 23 months ago by
cathalgking
▴ 10
1
vote
2
replies
1.5k
views
What number components should I use if I want to show 2D and 3D UMAP
scater
UAMP
scRNAseq
2.2 years ago
Guandong Shang
▴ 40
0
votes
4
replies
2.5k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater
batchelor
scRNAseq
fastMNN
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
Guandong Shang
▴ 40
3
votes
2
replies
2.1k
views
FeaturePlot in scater
scater
OSCA
2.5 years ago
Guandong Shang
▴ 40
5
votes
4
replies
2.2k
views
scater runUMAP
scater
runUMAP
2.7 years ago
jianhai.zhang
• 0
2
votes
1
reply
1.5k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment
scran
scater
updated 2.7 years ago by
Basti
▴ 780 • written 2.7 years ago by
Lucky
• 0
0
votes
6
replies
3.4k
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 2.8 years ago by
alan.ocallaghan
▴ 160 • written 2.9 years ago by
tinyimp80
• 0
2
votes
7
replies
2.1k
views
calculateTSNE with large dataset
runTSNE
calculateTSNE
scater
updated 2.8 years ago by
mikhael.manurung
▴ 280 • written 2.8 years ago by
alaihd
▴ 10
1
vote
2
replies
1.2k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment
scater
ExperimentalDesign
scran
2.8 years ago
msn
▴ 10
1
vote
2
replies
1.4k
views
More than 3 dimensions in runTSNE
dimensions
scater
runTSNE
3.1 years ago
jianhai.zhang
• 0
3
votes
3
replies
2.0k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater
SingleCellExperiment
BiocParallel
scuttle
scran
3.2 years ago • updated 3.1 years ago
enricoferrero
▴ 660
2
votes
3
replies
1.5k
views
scater::plotHeatmap with swap_rownames gives error
scater
3.2 years ago
enricoferrero
▴ 660
2
votes
2
replies
1.7k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA
BPPARAM
scater
BiocParallel
runPCA
3.5 years ago
doliv071
• 0
2
votes
3
replies
1.6k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment
scater
updated 3.9 years ago by
alan.ocallaghan
▴ 160 • written 3.9 years ago by
rogerbear
• 0
3
votes
2
replies
2.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell
SingleCellExperiment
scater
3.9 years ago
camerond
• 0
4
votes
5
replies
2.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran
SingleCellExperiment
scuttle
scater
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
enricoferrero
▴ 660
2
votes
7
replies
3.3k
views
How to run runNMF in parallel?
scater
single
SingleCellExperiment
updated 3.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
p.joshi
▴ 40
0
votes
0
replies
973
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater
singlecell
scran
BatchEffect
4.1 years ago
hamza_karakurt
▴ 60
3
votes
3
replies
2.7k
views
What lengths are used to calculate TPM in "scater" package
scater
calculateTPM
RNAseq
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Matan G.
▴ 60
5
votes
5
replies
2.0k
views
Running NMF for single cell
NMF
scater
4.2 years ago
lirongrossmann
▴ 50
0
votes
1
reply
1.3k
views
Change annotation colors plotHeatmap
scater
plotHeatmap
4.3 years ago
simone.avesani22
• 0
5
votes
4
replies
7.1k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran
scater
scuttle
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
enricoferrero
▴ 660
3
votes
1
reply
1.4k
views
Scaling option in fastMNN
fastmnn
scater
batchelor
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
ATpoint
★ 4.6k
0
votes
1
reply
1.7k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment
sce
scater
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
bharris
• 0
0
votes
4
replies
1.5k
views
Issues with normalizing viral-infected single cell data
scan
scater
single cell
normalization
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Jenny Drnevich
★ 2.0k
2
votes
4
replies
2.9k
views
Quality control in SingleCellExperiment
SingleCellExperiment
scater
sce
quality control
updated 3.9 years ago by
1498554536
• 0 • written 4.8 years ago by
Linda
• 0
0
votes
1
reply
1.3k
views
scater cbind for singlecellexperiment objects problem
scater
SingleCellExperiment
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
santos22903
• 0
4
votes
1
reply
1.4k
views
could not find function "plotQC" in scater package
scater
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
moldach
▴ 20
2
votes
1
reply
2.4k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq
scater
scran
rna-seq
MNN
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
hamza_karakurt
▴ 60
4
votes
4
replies
3.1k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
Bogdan
▴ 670
4
votes
4
replies
1.9k
views
scRNA-seq : Classification of cell cycle phase
scater
scran
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Bogdan
▴ 670
3
votes
7
replies
2.4k
views
scRNA-seq : runPCA() and denoisePCA()
scater
scran
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Bogdan
▴ 670
1
vote
4
replies
1.8k
views
number of cell clusters in scRNA-seq
scran
scater
sc3
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Bogdan
▴ 670
0
votes
7
replies
2.6k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater
limma
scde
scran
sc3
5.5 years ago
Bogdan
▴ 670
0
votes
1
reply
1.0k
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
5.5 years ago
hamza_karakurt
▴ 60
2
votes
1
reply
1.3k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater
BiocSingular
DelayedArray
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
kevin.rue
▴ 350
2
votes
4
replies
4.1k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater
scran
singlecellexperiment
normalize
qc
updated 2.7 years ago by
Dayme
• 0 • written 5.7 years ago by
kushshah
▴ 10
8
votes
4
replies
3.0k
views
Usage of doubletCells() function before or after the batch correction?
scater
scran
scRNA-Seq
doubletCells
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
hamza_karakurt
▴ 60
2
votes
3
replies
1.9k
views
Unable to change point size in plotExpression()
scater
plotexpression
singlecellexperiment
plotting
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
kushshah
▴ 10
4
votes
5
replies
2.1k
views
Using SC3 with batch corrected MNN values
SC3
Scater
Scran
scRNA-Seq
Batch Correction
updated 5.7 years ago by
Vladimir Kiselev
▴ 150 • written 5.7 years ago by
hamza_karakurt
▴ 60
7
votes
3
replies
3.9k
views
Log2(RPKM) counts in Bioconductor
rpkm
scater
calcaverage
R
expression
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
kushshah
▴ 10
50 results • Page
1 of 1
Recent ...
Replies
Comment: Cross-validation with multiple control subgroups in limma
by
Ali Barry
▴ 40
Thanks so much for taking the time here, the insights are much appreciated. I suspected I'd have to ad hoc compare results if I did repeat …
Answer: Cross-validation with multiple control subgroups in limma
by
Gordon Smyth
52k
limma doesn't do cross-validation or resampling. Like most classical linear modeling procedures in statistics, limma uses a statistical mod…
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
by
Robert Castelo
★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS
by
Aidan
▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings?
by
Michael Love
43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Votes
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio
C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
Awards
• All
Popular Question
to
Ali Barry
▴ 40
Popular Question
to
gabriel.hoffman
▴ 170
Popular Question
to
Jenny Drnevich
★ 2.0k
Popular Question
to
martin.grigorov
▴ 10
Scholar
to
James W. MacDonald
67k
Locations
• All
WEHI, Melbourne, Australia,
21 minutes ago
The city by the bay,
53 minutes ago
Germany,
2 hours ago
EMBL Heidelberg,
2 hours ago
UPF, Barcelona, Spain,
2 hours ago
Traffic: 616 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