Showing : singlecellexperiment • reset
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 7 days ago by ▴ 750 • written 11 days ago by • 0
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120
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
3 months ago Ibrahim • 0
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0
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185
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
3 months ago info ▴ 10
2
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2
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474
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 4 months ago by ▴ 10
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1
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866
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 months ago by ★ 28k • written 5 months ago by • 0
0
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1
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351
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T cell subtype annotation
SingleCellExperiment
updated 6 months ago by 67k • written 6 months ago by • 0
0
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1
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1.4k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 7 months ago by • 0 • written 7 months ago by • 0
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
7 months ago Stefano Mangiola ▴ 20
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4
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668
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
7 months ago vohara4 • 0
4
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1
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1.1k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 12 months ago by 67k • written 12 months ago by ▴ 20
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6
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1.1k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
12 months ago Dario Strbenac ★ 1.5k
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362
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rpk per cell saved in SCE object.
SingleCellExperiment
12 months ago JalapenoCornbread • 0
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2
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1.4k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
13 months ago elgomez • 0
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7
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2.1k
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Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 14 months ago by • 0
0
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1
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806
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 15 months ago by • 0
2
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5
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1.4k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
17 months ago duez.tolga • 0
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2
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1.6k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
19 months ago Matvii Mykhailichenko • 0
0
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2
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1.4k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
19 months ago Lluís Revilla Sancho ▴ 760
1
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3
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3.1k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
21 months ago mollyab12 • 0
0
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1
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1.6k
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Rename colData column
SingleCellExperiment colData rename
updated 23 months ago by ▴ 780 • written 23 months ago by ▴ 10
2
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3
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2.1k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.0 years ago by ▴ 20 • written 6.0 years ago by ▴ 10
2
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3
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2.2k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago • updated 2.3 years ago merv ▴ 140
2
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2
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1.0k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.4 years ago k1m ▴ 20
2
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4
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1.2k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.4 years ago Romina • 0
1
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1
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1.7k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.4 years ago by ▴ 750 • written 2.4 years ago by ▴ 140
5
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1
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3.5k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago merv ▴ 140
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0
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1.4k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.4 years ago merv ▴ 140
4
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3
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2.2k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.5 years ago by 67k • written 2.5 years ago by ▴ 10
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1
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1.3k
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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 2.6 years ago by ★ 4.6k • written 2.6 years ago by • 0
2
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5
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5.4k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 23 months ago by • 0 • written 2.8 years ago by ▴ 10
2
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1
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1.5k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.8 years ago by ▴ 780 • written 2.8 years ago by • 0
1
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2
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1.2k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.0 years ago • updated 2.9 years ago msn ▴ 10
0
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1
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892
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
2
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2
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1.5k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.1 years ago by ★ 4.6k • written 3.1 years ago by ▴ 40
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0
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801
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.2 years ago Núria • 0
1
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2
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1.1k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.2 years ago Fatima • 0
3
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3
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2.1k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.3 years ago • updated 3.2 years ago enricoferrero ▴ 660
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1
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3.3k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.4 years ago by ★ 4.6k • written 3.4 years ago by • 0
2
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5
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5.9k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.7 years ago by ▴ 60 • written 3.7 years ago by ▴ 20
2
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3
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1.7k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.0 years ago by ▴ 160 • written 4.0 years ago by • 0
3
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2
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2.8k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.0 years ago camerond • 0
0
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7
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2.6k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.0 years ago • updated 3.9 years ago bge • 0
1
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3
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2.2k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
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5
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3.0k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 660
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2
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1.6k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.1 years ago achaillon • 0
1
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3
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1.3k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.1 years ago by ▴ 70 • written 4.1 years ago by • 0
2
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3
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2.0k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.1 years ago achaillon • 0
0
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2
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1.7k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.1 years ago jirkanov • 0
2
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2
replies
2.5k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.1 years ago lirongrossmann ▴ 50
0
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1
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1.1k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Bioconductor Course, Kenya 2025: Applications Open!
Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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