Showing : SingleCellExperiment • reset
3
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2
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 4 days ago by ▴ 40 • written 6 weeks ago by • 0
0
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0
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144
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
4 months ago Ibrahim • 0
0
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0
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225
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
4 months ago info ▴ 10
2
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2
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534
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 5 months ago by ▴ 10
1
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1
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1.1k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 6 months ago by ★ 28k • written 6 months ago by • 0
0
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1
reply
380
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T cell subtype annotation
SingleCellExperiment
updated 7 months ago by 68k • written 7 months ago by • 0
0
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1
reply
1.7k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 8 months ago by • 0 • written 8 months ago by • 0
0
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0
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600
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
8 months ago Stefano Mangiola ▴ 40
0
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4
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741
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
8 months ago vohara4 • 0
4
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1
reply
1.3k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 13 months ago by 68k • written 13 months ago by ▴ 20
4
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6
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1.2k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
13 months ago Dario Strbenac ★ 1.6k
0
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0
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392
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rpk per cell saved in SCE object.
SingleCellExperiment
13 months ago JalapenoCornbread • 0
1
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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
14 months ago elgomez • 0
0
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7
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2.2k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 15 months ago by • 0
0
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1
reply
845
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 17 months ago by • 0
2
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5
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1.4k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
19 months ago • updated 18 months ago duez.tolga • 0
0
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2
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1.7k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
20 months ago Matvii Mykhailichenko • 0
0
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2
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1.5k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
20 months ago Lluís Revilla Sancho ▴ 760
1
vote
3
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3.3k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
22 months ago mollyab12 • 0
0
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1
reply
1.7k
views
Rename colData column
SingleCellExperiment colData rename
updated 2.0 years ago by ▴ 780 • written 2.0 years ago by ▴ 10
2
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3
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2.2k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.1 years ago by ▴ 40 • written 6.1 years ago by ▴ 10
4
votes
3
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2.3k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.5 years ago • updated 2.4 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
2.5 years ago k1m ▴ 20
2
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4
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1.3k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.5 years ago Romina • 0
1
vote
1
reply
1.8k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.5 years ago by ▴ 750 • written 2.5 years ago by ▴ 150
5
votes
1
reply
3.5k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.5 years ago merv ▴ 150
0
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0
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1.5k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.5 years ago merv ▴ 150
4
votes
3
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2.2k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
0
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1
reply
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 2.7 years ago by ★ 4.7k • written 2.7 years ago by • 0
2
votes
5
replies
5.7k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.0 years ago by • 0 • written 2.9 years ago by ▴ 10
2
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1
reply
1.6k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.9 years ago by ▴ 780 • written 2.9 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 msn ▴ 10
0
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1
reply
918
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
2
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2
replies
1.5k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.2 years ago by ★ 4.7k • written 3.2 years ago by ▴ 40
0
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0
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838
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.3 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
3.3 years ago Fatima • 0
3
votes
3
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2.1k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.4 years ago • updated 3.3 years ago enricoferrero ▴ 680
0
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1
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3.4k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.5 years ago by ★ 4.7k • written 3.5 years ago by • 0
2
votes
5
replies
6.1k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.8 years ago by ▴ 60 • written 3.8 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 4.1 years ago by ▴ 160 • written 4.1 years ago by • 0
3
votes
2
replies
3.0k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.1 years ago camerond • 0
0
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7
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2.7k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.1 years ago • updated 4.0 years ago bge • 0
1
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3
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2.3k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.1 years ago by ★ 28k • written 4.2 years ago by ▴ 10
4
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5
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3.2k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 680
0
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2
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1.6k
views
from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.2 years ago achaillon • 0
1
vote
3
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1.4k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.2 years ago by ▴ 70 • written 4.2 years ago by • 0
2
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3
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2.1k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.2 years ago achaillon • 0
0
votes
2
replies
1.8k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.2 years ago jirkanov • 0
2
votes
2
replies
2.7k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.2 years ago lirongrossmann ▴ 50
0
votes
1
reply
1.1k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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