Showing : singleCellExperiment • reset
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 8 weeks ago by ★ 4.0k • written 4 months ago by • 0
1
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2
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474
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 10 weeks ago by ★ 4.0k • written 3 months ago by • 0
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175
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
4 months ago Ludwig Geistlinger ▴ 80
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9
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4.7k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 11 weeks ago by • 0 • written 6 months ago by ▴ 10
4
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17
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6.1k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 7 months ago by ★ 5.0k • written 8 months ago by ▴ 10
1
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3
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1.3k
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
8 months ago • updated 7 months ago Konstantinos Yeles ▴ 90
3
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2
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835
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 10 months ago by ▴ 40 • written 12 months ago by • 0
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0
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410
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
15 months ago Ibrahim • 0
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0
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598
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
15 months ago info ▴ 10
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2
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906
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 16 months ago by ▴ 10
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1
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2.5k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 17 months ago by ★ 29k • written 17 months ago by • 0
0
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1
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719
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T cell subtype annotation
SingleCellExperiment
updated 18 months ago by 68k • written 18 months ago by • 0
0
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1
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4.2k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 18 months ago by • 0 • written 19 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
19 months ago Stefano Mangiola ▴ 40
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4
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1.3k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
19 months ago vohara4 • 0
4
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1
reply
2.0k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 24 months ago by 68k • written 24 months ago by ▴ 20
4
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6
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1.6k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
2.0 years ago • updated 24 months ago Dario Strbenac ★ 1.6k
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557
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rpk per cell saved in SCE object.
SingleCellExperiment
2.0 years ago JalapenoCornbread • 0
1
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2
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1.9k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
2.1 years ago elgomez • 0
0
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10
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3.9k
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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 2.1 years ago by • 0
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1
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1.1k
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.3 years ago by • 0
2
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5
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1.9k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.4 years ago duez.tolga • 0
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2
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2.1k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.6 years ago Matvii Mykhailichenko • 0
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2
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2.0k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.6 years ago Lluís Revilla Sancho ▴ 760
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3
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4.0k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.7 years ago mollyab12 • 0
0
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1
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2.2k
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Rename colData column
SingleCellExperiment colData rename
updated 2.9 years ago by ▴ 780 • written 2.9 years ago by ▴ 10
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3
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2.6k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 3.0 years ago by ▴ 40 • written 7.0 years ago by ▴ 10
4
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3
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2.9k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago • updated 3.3 years ago merv ▴ 150
2
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4
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2.2k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 5 months ago by • 0 • written 3.4 years ago by ▴ 20
2
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4
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1.7k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.4 years ago Romina • 0
1
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1
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2.5k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.4 years ago by ▴ 760 • written 3.4 years ago by ▴ 150
5
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1
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4.1k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago merv ▴ 150
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0
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1.9k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago merv ▴ 150
4
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3
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2.8k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
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1
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1.6k
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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 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
votes
5
replies
6.6k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.9 years ago by • 0 • written 3.7 years ago by ▴ 10
2
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1
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2.0k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.8 years ago by ▴ 780 • written 3.8 years ago by • 0
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2
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1.6k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.9 years ago msn ▴ 10
0
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1
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1.1k
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 4.0 years ago by 68k • written 4.0 years ago by • 0
2
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2
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1.8k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by ▴ 40
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0
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1.1k
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
4.1 years ago Núria • 0
1
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2
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1.4k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.2 years ago Fatima • 0
3
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3
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2.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.2 years ago enricoferrero ▴ 680
0
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1
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3.9k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
2
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5
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7.2k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.6 years ago by ▴ 60 • written 4.7 years ago by ▴ 20
2
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3
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2.1k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.9 years ago by ▴ 160 • written 4.9 years ago by • 0
3
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2
replies
3.6k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
5.0 years ago • updated 4.9 years ago camerond • 0
0
votes
7
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3.3k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
5.0 years ago • updated 4.9 years ago bge • 0
1
vote
3
replies
2.6k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 10
4
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5
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4.0k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 680
93 results • Page 1 of 2
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Comment: DESeq2 - how many surrogate variables from svaseq, use of lfcshrink by ja569116 • 0
Hi @atpoint Thanks for the information. Could you please expand on when to use adjusted p-values vs nominal p-values. My understanding was …
Answer: limpa analysis advice by Gordon Smyth 53k
It is actually very hard to estimate the DPC from observed data, because the curve is function of unobserved intensities rather than a func…
Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
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Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
Answer: When to use edgeR or limma
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
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