Showing : SingleCellExperiment • reset
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 7 weeks ago by • 0
1
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5
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474
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
3 months ago duez.tolga • 0
0
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2
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499
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
5 months ago Matvii Mykhailichenko • 0
0
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2
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456
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
5 months ago Lluís Revilla Sancho ▴ 720
1
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3
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1.1k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
7 months ago mollyab12 • 0
0
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1
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659
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Rename colData column
SingleCellExperiment colData rename
updated 9 months ago by ▴ 740 • written 9 months ago by ▴ 10
2
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3
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1.3k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 10 months ago by ▴ 10 • written 4.8 years ago by ▴ 10
2
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3
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1.1k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
14 months ago merv ▴ 100
2
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2
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576
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
14 months ago k1m ▴ 20
2
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4
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717
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
14 months ago Romina • 0
1
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1
reply
791
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 15 months ago by ▴ 650 • written 15 months ago by ▴ 100
4
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1
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1.5k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
15 months ago merv ▴ 100
0
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0
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626
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
15 months ago merv ▴ 100
4
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3
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1.0k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 16 months ago by 64k • written 16 months ago by ▴ 10
0
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1
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759
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Use of Scater for QC in scRNA-seq: How to remove cells with less than certain number of genes supported with certain number of reads
SingleCellExperiment
updated 17 months ago by ★ 3.6k • written 17 months ago by • 0
2
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5
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3.2k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 9 months ago by • 0 • written 19 months ago by ▴ 10
2
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1
reply
864
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 20 months ago by ▴ 740 • written 20 months ago by • 0
1
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2
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753
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
21 months ago msn ▴ 10
0
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1
reply
615
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 22 months ago by 64k • written 22 months ago by • 0
2
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2
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988
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 23 months ago by ★ 3.6k • written 23 months ago by ▴ 40
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0
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502
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
24 months ago Núria • 0
1
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2
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695
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
2.0 years ago Fatima • 0
3
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3
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1.4k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.1 years ago enricoferrero ▴ 660
0
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1
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2.1k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.3 years ago by ★ 3.6k • written 2.3 years ago by • 0
2
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5
replies
4.2k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 2.5 years ago by ▴ 60 • written 2.6 years ago by ▴ 20
2
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3
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1.1k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 2.8 years ago by ▴ 120 • written 2.8 years ago by • 0
3
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2
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1.8k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
2.8 years ago camerond • 0
0
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7
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1.8k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
2.8 years ago bge • 0
1
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3
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1.6k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 10
4
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5
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1.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 2.9 years ago by ★ 28k • written 2.9 years ago by ▴ 660
0
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2
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992
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
2.9 years ago achaillon • 0
1
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3
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876
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 2.9 years ago by ▴ 70 • written 2.9 years ago by • 0
1
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3
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1.3k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.0 years ago • updated 2.9 years ago achaillon • 0
0
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2
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1.2k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.0 years ago jirkanov • 0
1
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2
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1.6k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.0 years ago lirongrossmann ▴ 40
0
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1
reply
709
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.1 years ago by ★ 28k • written 3.1 years ago by ▴ 40
2
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7
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2.1k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.0 years ago by ★ 28k • written 3.1 years ago by ▴ 40
0
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6
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2.1k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 80
1
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1
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1.0k
views
Biological replicates in single cell experiments DE
singleCellExperiment
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
0
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4
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1.1k
views
marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 40
0
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0
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637
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.3 years ago lirongrossmann ▴ 80
0
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3
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1.7k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 40
1
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2
replies
1.6k
views
ident function in sce
SingleCellExperiment cluster identities sce
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
0
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1
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985
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 3.6 years ago by ★ 28k • written 3.6 years ago by • 0
2
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4
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1.9k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 2.8 years ago by • 0 • written 3.7 years ago by • 0
0
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2
replies
1.0k
views
Can't Load SingleCellExperiment Object
software error SingleCellExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
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1
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830
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scater cbind for singlecellexperiment objects problem
scater SingleCellExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
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2
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1.4k
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
4.1 years ago albadrs.93 ▴ 10
4
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2
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1.3k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment scran limma simpleSingleCell
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
2
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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 • 0 • written 4.6 years ago by ▴ 10
50 results • Page 1 of 1
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Answer: NCBI protein to NCBI cDNA (Ensembl conversions would be great as well) in R by James W. MacDonald 64k
I don't know what you mean by 'cDNA value'. That could mean any number of things, I suppose, particularly if you don't know what cDNA is (p…
Comment: How can we use the organism database created by makeorgPackageFromNCBI to KEGG a by Guido Hooiveld ★ 3.8k
What did you try yourselves? Again, please show your code....!! For KEGG-based analysis you can make use of the convenience functions `enr…
Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by Basti ▴ 740
The image is blurred, but you need to follow ATpoint advice and restart the entire analysis using a clean environment.
Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by 486342583 • 0
This is my running code myDMP <- champ.DMP(beta = myNormA, pheno = myLoad$pd$Sample_Group, …
Comment: Deleted:No significant MVPs with a BH adjusted P-value below 0.05 by 486342583 • 0
![enter image description here][1] Thank you for your reply. I am a beginner. What I meant was that I could have obtained this image yester…
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A: DSS understanding delta option and posterior probability
Comment: Ensembl down???
Answer: How should I run ssGSEA Hallmark Enrichment Analysis?
Answer: tximport: Error in is(txi, "list") : argument "txi" is missing, with no default
Comment: Problem loading HDF5Array in R 4.3.2
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