Showing : singlecellexperiment • reset
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
16 days ago Ibrahim • 0
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96
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
28 days ago info ▴ 10
2
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2
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346
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 9 weeks ago by ▴ 10
1
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1
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527
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 12 weeks ago by ★ 28k • written 3 months ago by • 0
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1
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287
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T cell subtype annotation
SingleCellExperiment
updated 3 months ago by 67k • written 3 months ago by • 0
0
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1
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913
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 4 months ago by • 0 • written 4 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
4 months ago Stefano Mangiola ▴ 20
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4
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550
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
4 months ago vohara4 • 0
4
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1
reply
918
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 9 months ago by 67k • written 9 months ago by ▴ 20
4
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6
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949
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
9 months ago Dario Strbenac ★ 1.5k
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318
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rpk per cell saved in SCE object.
SingleCellExperiment
9 months ago JalapenoCornbread • 0
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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
10 months ago elgomez • 0
0
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4
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1.4k
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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 19 days ago by • 0 • written 11 months ago by • 0
0
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1
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730
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 13 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
15 months ago duez.tolga • 0
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2
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1.4k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
16 months ago Matvii Mykhailichenko • 0
0
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2
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1.2k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
16 months ago Lluís Revilla Sancho ▴ 760
1
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3
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2.7k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
18 months ago mollyab12 • 0
0
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1
reply
1.5k
views
Rename colData column
SingleCellExperiment colData rename
updated 20 months ago by ▴ 780 • written 20 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 21 months ago by ▴ 20 • written 5.8 years ago by ▴ 10
2
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3
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2.0k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.2 years ago • updated 2.1 years ago merv ▴ 140
2
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2
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984
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.2 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
2.2 years ago Romina • 0
1
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1
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1.6k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.2 years ago by ▴ 740 • written 2.2 years ago by ▴ 140
5
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1
reply
3.2k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.2 years ago merv ▴ 140
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0
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1.3k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.2 years ago merv ▴ 140
4
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3
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2.0k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.3 years ago by 67k • written 2.3 years ago by ▴ 10
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1
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1.2k
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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 2.4 years ago by ★ 4.5k • written 2.4 years ago by • 0
2
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5
replies
5.1k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 20 months ago by • 0 • written 2.5 years ago by ▴ 10
2
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1
reply
1.4k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.6 years ago by ▴ 780 • written 2.6 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
2.7 years ago msn ▴ 10
0
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1
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853
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.8 years ago by 67k • written 2.8 years ago by • 0
2
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2
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1.4k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.9 years ago by ★ 4.5k • written 2.9 years ago by ▴ 40
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0
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761
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.9 years ago Núria • 0
1
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2
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1.0k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.0 years ago Fatima • 0
3
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3
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2.0k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.0 years ago enricoferrero ▴ 660
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1
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3.1k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.2 years ago by ★ 4.5k • written 3.2 years ago by • 0
2
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5
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5.6k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.4 years ago by ▴ 60 • written 3.5 years ago by ▴ 20
2
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3
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1.6k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.7 years ago by ▴ 160 • written 3.7 years ago by • 0
3
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2
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2.7k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.8 years ago • updated 3.7 years ago camerond • 0
0
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7
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2.5k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.8 years ago • updated 3.7 years ago bge • 0
1
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3
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2.1k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 10
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5
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2.8k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.8 years ago by ★ 28k • written 3.8 years ago by ▴ 660
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2
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1.5k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
3.9 years ago achaillon • 0
1
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3
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1.3k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.9 years ago by ▴ 70 • written 3.9 years ago by • 0
2
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3
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1.9k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.9 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
3.9 years ago jirkanov • 0
2
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2
replies
2.4k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.9 years ago lirongrossmann ▴ 50
0
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1
reply
1.0k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.0 years ago by ★ 28k • written 4.0 years ago by ▴ 50
2
votes
7
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3.2k
views
How to run runNMF in parallel?
scater single SingleCellExperiment
updated 3.0 years ago by ★ 28k • written 4.0 years ago by ▴ 40
50 results • Page 1 of 1
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Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
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A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
A: How does edgeR cpm function calculate log(CPM) values?
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