Showing : SingleCellExperiment • reset
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 8 weeks ago by ▴ 40 • written 3 months ago by • 0
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
6 months ago Ibrahim • 0
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290
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
6 months ago info ▴ 10
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2
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597
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 7 months ago by ▴ 10
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1.5k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 8 months ago by ★ 28k • written 8 months ago by • 0
0
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1
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417
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T cell subtype annotation
SingleCellExperiment
updated 9 months ago by 68k • written 9 months ago by • 0
0
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1
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2.3k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 9 months ago by • 0 • written 10 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
10 months ago Stefano Mangiola ▴ 40
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4
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
10 months ago vohara4 • 0
4
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1
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1.5k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 15 months ago by 68k • written 15 months ago by ▴ 20
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6
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1.3k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
15 months ago Dario Strbenac ★ 1.6k
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409
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rpk per cell saved in SCE object.
SingleCellExperiment
15 months ago JalapenoCornbread • 0
1
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2
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1.5k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
16 months ago elgomez • 0
0
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3.2k
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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
updated 7 days ago by • 0 • written 16 months ago by • 0
0
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888
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 18 months ago by • 0
2
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5
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1.5k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
20 months ago duez.tolga • 0
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2
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1.8k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
22 months ago Matvii Mykhailichenko • 0
0
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2
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1.6k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
22 months ago Lluís Revilla Sancho ▴ 760
1
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3
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3.5k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.0 years ago • updated 24 months ago mollyab12 • 0
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1
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1.8k
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Rename colData column
SingleCellExperiment colData rename
updated 2.2 years ago by ▴ 780 • written 2.2 years ago by ▴ 10
2
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3
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2.3k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.3 years ago by ▴ 40 • written 6.2 years ago by ▴ 10
4
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3
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2.5k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.6 years ago merv ▴ 150
2
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2
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1.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.6 years ago k1m ▴ 20
2
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4
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1.3k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.6 years ago Romina • 0
1
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1
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2.0k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.6 years ago by ▴ 750 • written 2.6 years ago by ▴ 150
5
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1
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3.7k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.6 years ago merv ▴ 150
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1.6k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.6 years ago merv ▴ 150
4
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3
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2.3k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.7 years ago by 68k • written 2.7 years ago by ▴ 10
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1
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1.4k
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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 2.8 years ago by ★ 4.8k • written 2.8 years ago by • 0
2
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5
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6.0k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.2 years ago by • 0 • written 3.0 years ago by ▴ 10
2
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1
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1.6k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.1 years ago by ▴ 780 • written 3.1 years ago by • 0
1
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2
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1.3k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.2 years ago msn ▴ 10
0
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1
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939
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.3 years ago by 68k • written 3.3 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 3.4 years ago by ★ 4.8k • written 3.4 years ago by ▴ 40
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0
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872
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.4 years ago Núria • 0
1
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2
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1.2k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.5 years ago • updated 3.4 years ago Fatima • 0
3
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3
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2.2k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.5 years ago enricoferrero ▴ 680
0
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1
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3.5k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.7 years ago by ★ 4.8k • written 3.7 years ago by • 0
2
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5
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6.4k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.9 years ago by ▴ 60 • written 4.0 years ago by ▴ 20
2
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3
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1.8k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.2 years ago by ▴ 160 • written 4.2 years ago by • 0
3
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2
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3.1k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.2 years ago camerond • 0
0
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7
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2.8k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.2 years ago bge • 0
1
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3
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2.3k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 10
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5
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3.4k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 680
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2
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1.7k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.3 years ago achaillon • 0
1
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3
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1.4k
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.3 years ago by ▴ 70 • written 4.3 years ago by • 0
2
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3
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2.1k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.4 years ago • updated 4.3 years ago achaillon • 0
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2
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1.8k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.4 years ago jirkanov • 0
2
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2
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2.8k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.4 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 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: error in ChAMP loading file by janwilseo • 0
Any update on this post? I also had an issue with this. [erosion control](https://charlestonhydroseeding.com/)
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Two things. First, the order of your term2gene is backwards (should be term and then gene, like the name), and by default `enricher` adjust…
Comment: Controlling for batch and estrus cycle using DESeq2 in RNA-seq analysis by donnycrimson • 0
One potential workaround might be to adjust for these factors using a combination of design matrices perhaps including batch as a covariate…
Comment: DESeq2 Design controlling for gender by donnycrimson • 0
On a lighter note, while you are tackling such complex data, you might enjoy a quick break playing the [Slope Game](https://slopegame.lol)…
Comment: MetaDE.pvalue: Error in xj[i]: invalid subscript type 'list' by donnycrimson • 0
Have you considered streamlining how you handle data input to mitigate these issues. It might help to define the parameters more strictly …
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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