Showing : scater • reset
0
votes
4
replies
783
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
3
votes
3
replies
1.8k
views
Function 'sexp_as_cholmod_sparse' doesn't exist in the package 'Matrix'
scater runPCA
updated 12 months ago by ▴ 160 • written 12 months ago by • 0
2
votes
1
reply
710
views
Existence of Bioconductor versus Seurat Software Ecosystems Quantitative Comparison
scran bluster scater scuttle
updated 12 months ago by ★ 4.8k • written 12 months ago by ★ 1.6k
3
votes
3
replies
1.6k
views
plotUMAP Gene Set Faceted
scater
updated 14 months ago by ▴ 160 • written 14 months ago by ★ 1.6k
1
vote
1
reply
732
views
plotUMAP and ggplotly Cell IDs Display
scater
updated 14 months ago by ▴ 160 • written 14 months ago by ★ 1.6k
1
vote
7
replies
9.2k
views
scater runUMAP fails with error "function 'as_cholmod_sparse' not provided by package 'Matrix'"
runUMAP scater Matrix
updated 13 months ago by 16k • written 16 months ago by ▴ 10
0
votes
3
replies
1.8k
views
Is logNormCounts log2 normalised counts as default?
scuttle scater
updated 19 months ago by ★ 4.8k • written 19 months ago by • 0
0
votes
6
replies
1.3k
views
plotHeatmap annotation error
plotHeatmap scater
21 months ago Alina • 0
1
vote
0
replies
2.3k
views
Convert SpatialExperiment Object to Seurat Object
scuttle scater seurat SpatialExperiment
2.2 years ago cathalgking ▴ 10
0
votes
1
reply
1.0k
views
cell_count column in SpatialExperiment Object
scuttle scater SpatialExperiment
updated 2.2 years ago by ▴ 160 • written 2.2 years ago by ▴ 10
1
vote
2
replies
1.7k
views
What number components should I use if I want to show 2D and 3D UMAP
scater UAMP scRNAseq
2.5 years ago Guandong Shang ▴ 40
0
votes
4
replies
2.7k
views
how to make the "reconstructed" value in intergated scRNA-seq UMAP plot more readable
scater batchelor scRNAseq fastMNN
updated 2.7 years ago by ★ 28k • written 2.7 years ago by ▴ 40
3
votes
2
replies
2.4k
views
FeaturePlot in scater
scater OSCA
2.8 years ago Guandong Shang ▴ 40
5
votes
4
replies
2.4k
views
scater runUMAP
scater runUMAP
3.0 years ago jianhai.zhang • 0
2
votes
1
reply
1.6k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by • 0
0
votes
6
replies
3.7k
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 3.1 years ago by ▴ 160 • written 3.1 years ago by • 0
2
votes
7
replies
2.3k
views
calculateTSNE with large dataset
runTSNE calculateTSNE scater
updated 3.1 years ago by ▴ 280 • written 3.1 years ago by ▴ 10
1
vote
2
replies
1.3k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.1 years ago msn ▴ 10
1
vote
2
replies
1.5k
views
More than 3 dimensions in runTSNE
dimensions scater runTSNE
3.4 years ago jianhai.zhang • 0
3
votes
3
replies
2.2k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.4 years ago enricoferrero ▴ 680
2
votes
3
replies
1.6k
views
scater::plotHeatmap with swap_rownames gives error
scater
3.5 years ago • updated 3.4 years ago enricoferrero ▴ 680
2
votes
2
replies
1.8k
views
scater::calculatePCA error when using BPPARAM = MulticoreParam
calculatePCA BPPARAM scater BiocParallel runPCA
3.8 years ago doliv071 • 0
2
votes
3
replies
1.7k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.1 years ago by ▴ 160 • written 4.1 years ago by • 0
3
votes
2
replies
3.0k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.2 years ago • updated 4.1 years ago camerond • 0
4
votes
5
replies
3.3k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 680
2
votes
7
replies
3.6k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 3.4 years ago by ★ 28k • written 4.4 years ago by ▴ 40
0
votes
0
replies
1.1k
views
Creating a stable batch-corrected scRNA-Seq data with multiple datasets and multiple integrations
scater singlecell scran BatchEffect
4.4 years ago hamza_karakurt ▴ 60
3
votes
3
replies
2.9k
views
What lengths are used to calculate TPM in "scater" package
scater calculateTPM RNAseq
updated 4.4 years ago by ★ 28k • written 4.5 years ago by ▴ 60
5
votes
5
replies
2.1k
views
Running NMF for single cell
NMF scater
4.5 years ago lirongrossmann ▴ 50
0
votes
1
reply
1.3k
views
Change annotation colors plotHeatmap
scater plotHeatmap
4.6 years ago simone.avesani22 • 0
5
votes
4
replies
7.8k
views
scRNA-seq pseudo-bulk differential expression analysis with pseudobulkDGE()
scran scater scuttle
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 680
3
votes
1
reply
1.5k
views
Scaling option in fastMNN
fastmnn scater batchelor
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ★ 4.8k
0
votes
1
reply
1.9k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.9 years ago by ★ 28k • written 4.9 years ago by • 0
0
votes
4
replies
1.6k
views
Issues with normalizing viral-infected single cell data
scan scater single cell normalization
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ★ 2.0k
2
votes
4
replies
3.2k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 4.2 years ago by • 0 • written 5.0 years ago by • 0
0
votes
1
reply
1.5k
views
scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
4
votes
1
reply
1.5k
views
could not find function "plotQC" in scater package
scater
updated 5.4 years ago by ★ 28k • written 5.4 years ago by ▴ 20
2
votes
1
reply
2.5k
views
Batch Corrections (MNN) with TPM values
scRNA-Seq scater scran rna-seq MNN
updated 5.5 years ago by ★ 28k • written 5.5 years ago by ▴ 60
4
votes
4
replies
3.3k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma edgeR simplesingleCell scran scater
updated 5.7 years ago by ★ 28k • written 5.7 years ago by ▴ 670
4
votes
4
replies
2.0k
views
scRNA-seq : Classification of cell cycle phase
scater scran
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
3
votes
7
replies
2.6k
views
scRNA-seq : runPCA() and denoisePCA()
scater scran
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
1
vote
4
replies
2.0k
views
number of cell clusters in scRNA-seq
scran scater sc3
updated 5.8 years ago by ★ 28k • written 5.8 years ago by ▴ 670
0
votes
7
replies
2.8k
views
differential expression between clusters (in distinct "treatments") in scRNAseq
scater limma scde scran sc3
5.8 years ago Bogdan ▴ 670
0
votes
1
reply
1.1k
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
5.8 years ago hamza_karakurt ▴ 60
2
votes
1
reply
1.4k
views
scater::runPCA() errors on DelayedMatrix (DelayedArray:::.check_Ops_vector_arg_length)
scater BiocSingular DelayedArray
updated 5.9 years ago by ★ 28k • written 5.9 years ago by ▴ 350
2
votes
4
replies
4.4k
views
ERROR - Size factors should be positive real numbers (using normalize() function)
scater scran singlecellexperiment normalize qc
updated 3.0 years ago by • 0 • written 6.0 years ago by ▴ 10
8
votes
4
replies
3.4k
views
Usage of doubletCells() function before or after the batch correction?
scater scran scRNA-Seq doubletCells
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 60
2
votes
3
replies
2.1k
views
Unable to change point size in plotExpression()
scater plotexpression singlecellexperiment plotting
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
4
votes
5
replies
2.3k
views
Using SC3 with batch corrected MNN values
SC3 Scater Scran scRNA-Seq Batch Correction
updated 6.0 years ago by ▴ 150 • written 6.0 years ago by ▴ 60
7
votes
3
replies
4.2k
views
Log2(RPKM) counts in Bioconductor
rpkm scater calcaverage R expression
updated 6.0 years ago by ★ 28k • written 6.0 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
I am not sure this has anything to do with it but i had to run the following as tximport wouldn't allow me to import abundance_1.h5 files t…
Comment: Error in H5Dclose(h5dataset) when trying to read in kallisto h5 files by Sofia • 0
1 2 3 Error in H5Dclose(h5dataset) : HDF5. Dataset. Unable to decrement reference count. ``` > traceback() 5: H5Dclose(h5dataset) 4: rhd…
Comment: DESeq2 model - How to test case/control time course model when taking account wi by wuwenhui2 • 0
Thanks, I figured it out.
Comment: Design Matrix with paired and independent samples plus RUVg Spike-in normalizati by Mei • 0
I have a similar experiment with 7 paired samples (T0 and T1) in each of 4 outcome groups. I am using RUVr combined with limma-voom, so I a…
Comment: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran by Arctic • 0
Many thanks for the link to the C++ code. I will see if I can find someone with C++ experience to help me with the code breakdown from her…
Votes
what the test method for enrichGO in clusterProfiler?
A: single-cells RNA-seq analysis by MAST with unbalanced group size
Comment: plyranges: find exact GRanges match keeping metadata columns
Answer: Help with the code for "BiocNeighbors::generic_find_knn() function used by scran
Is it possible to speed up VariantAnnotation's rowRanges function when converting to a dataframe?
Awards • All
Popular Question to Gordon Smyth 52k
Popular Question to Le • 0
Popular Question to Cen • 0
Popular Question to Marianna ▴ 20
Popular Question to Dunois • 0
Locations • All
Mexico, 56 minutes ago
Australia, 1 hour ago
United States, 3 hours ago
Seattle, WA, United States, 5 hours ago
Australia, 5 hours ago
Traffic: 840 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