Showing : SingleCellExperiment • reset
2
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
updated 9 days ago by 67k • written 9 days ago by ▴ 10
1
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2
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347
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 5 weeks ago by ★ 28k • written 5 weeks ago by • 0
0
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1
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231
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T cell subtype annotation
SingleCellExperiment
updated 8 weeks ago by 67k • written 8 weeks ago by • 0
0
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1
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584
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 10 weeks ago by • 0 • written 12 weeks ago by • 0
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
12 weeks ago Stefano Mangiola ▴ 10
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4
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464
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
3 months ago vohara4 • 0
4
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1
reply
742
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 7 months ago by 67k • written 7 months ago by ▴ 20
4
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6
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838
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
8 months ago • updated 7 months ago Dario Strbenac ★ 1.5k
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0
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280
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rpk per cell saved in SCE object.
SingleCellExperiment
8 months ago JalapenoCornbread • 0
1
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2
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1.2k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
9 months ago elgomez • 0
0
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3
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816
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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 9 months ago by • 0 • written 9 months ago by • 0
0
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1
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662
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 11 months ago by • 0
2
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5
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1.2k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
13 months ago duez.tolga • 0
0
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2
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1.2k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
14 months ago Matvii Mykhailichenko • 0
0
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2
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1.1k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
15 months ago Lluís Revilla Sancho ▴ 730
1
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3
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2.5k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
16 months ago mollyab12 • 0
0
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1
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1.4k
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Rename colData column
SingleCellExperiment colData rename
updated 19 months ago by ▴ 780 • written 19 months ago by ▴ 10
2
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3
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1.9k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 20 months ago by ▴ 10 • written 5.6 years ago by ▴ 10
2
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3
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1.9k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.0 years ago • updated 23 months ago merv ▴ 130
2
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2
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941
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.0 years ago k1m ▴ 20
2
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4
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1.1k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.0 years ago Romina • 0
1
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1
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1.4k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.0 years ago by ▴ 740 • written 2.0 years ago by ▴ 130
5
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1
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3.1k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.0 years ago merv ▴ 130
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0
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1.2k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.0 years ago merv ▴ 130
4
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3
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1.8k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.1 years ago by 67k • written 2.1 years ago by ▴ 10
0
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1
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1.1k
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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 2.2 years ago by ★ 4.4k • written 2.2 years ago by • 0
2
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5
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4.8k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 18 months ago by • 0 • written 2.4 years ago by ▴ 10
2
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1
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1.3k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by • 0
1
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2
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1.1k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.6 years ago msn ▴ 10
0
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1
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810
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.7 years ago by 67k • written 2.7 years ago by • 0
2
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2
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1.3k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.7 years ago by ★ 4.4k • written 2.8 years ago by ▴ 40
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0
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725
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.8 years ago Núria • 0
1
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2
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972
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
2.8 years ago Fatima • 0
3
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3
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1.9k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.9 years ago enricoferrero ▴ 660
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1
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3.0k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.1 years ago by ★ 4.4k • written 3.1 years ago by • 0
2
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5
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5.4k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.3 years ago by ▴ 60 • written 3.4 years ago by ▴ 20
2
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3
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1.5k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.6 years ago by ▴ 160 • written 3.6 years ago by • 0
3
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2
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2.6k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.6 years ago camerond • 0
0
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7
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2.4k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.6 years ago bge • 0
1
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3
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2.0k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 10
4
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5
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2.7k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 660
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2
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1.4k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
3.7 years ago achaillon • 0
1
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3
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1.2k
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.7 years ago by ▴ 70 • written 3.7 years ago by • 0
2
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3
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1.8k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.8 years ago • updated 3.7 years ago achaillon • 0
0
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2
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1.6k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.8 years ago jirkanov • 0
2
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2
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2.3k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.8 years ago lirongrossmann ▴ 50
0
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1
reply
962
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 50
2
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7
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3.0k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.8 years ago by ★ 28k • written 3.9 years ago by ▴ 40
0
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6
replies
2.9k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 80
1
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1
reply
1.3k
views
Biological replicates in single cell experiments DE
singleCellExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
50 results • Page 1 of 1
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Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
The odds ratio, not log FC. My bad.
Comment: When doing differential methylation using the sesame package, seems to only go by James W. MacDonald 67k
``` testResult$Eff_Condition > 0.1 ```
Comment: clusterProfiler: BgRatio N value does not match the size of the gene universe th by Fatima • 0
I identified 3804 genes with GO annotations. I put my liste of genes in this link [enter link description here][1] universe <- mapIds…
Comment: When doing differential methylation using the sesame package, seems to only go by ramiro.barrantes ▴ 10
Hello, Thank you. I absolutely respect what you mention about p-values and logFC, I was just going to tackle that soon and thank you for po…
Comment: QSEA:Error in h(simpleError(msg, call)) by kf • 0
genome(qseaSet@regions)<-"BSgenome.Hsapiens.UCSC.hg38" solve the problem
Votes
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: Question: How to Set Up Contrasts for Case-Control Analysis in Limma While Adjus
Answer: clusterProfiler: BgRatio N value does not match the size of the gene universe th
Answer: object 'hdac_targets' not found
Answer: object 'hdac_targets' not found
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