Showing : SingleCellExperiment • reset
3
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 5 weeks ago by ▴ 40 • written 11 weeks ago by • 0
0
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0
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169
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
5 months ago Ibrahim • 0
0
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0
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268
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
5 months ago info ▴ 10
2
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2
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572
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 7 months ago by ▴ 10
1
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1
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1.4k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 7 months ago by ★ 28k • written 8 months ago by • 0
0
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1
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409
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T cell subtype annotation
SingleCellExperiment
updated 8 months ago by 68k • written 8 months ago by • 0
0
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1
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2.0k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 9 months ago by • 0 • written 9 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
9 months ago Stefano Mangiola ▴ 40
0
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4
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785
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
9 months ago vohara4 • 0
4
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1
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1.4k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 14 months ago by 68k • written 14 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
14 months ago Dario Strbenac ★ 1.6k
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0
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402
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rpk per cell saved in SCE object.
SingleCellExperiment
14 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
15 months ago elgomez • 0
0
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7
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2.2k
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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
written 16 months ago by • 0
0
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1
reply
871
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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 • updated 19 months ago duez.tolga • 0
0
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2
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1.7k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
21 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
21 months ago Lluís Revilla Sancho ▴ 760
1
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3
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3.4k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
23 months ago mollyab12 • 0
0
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1
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1.8k
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Rename colData column
SingleCellExperiment colData rename
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by ▴ 10
2
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3
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2.2k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.2 years ago by ▴ 40 • written 6.2 years ago by ▴ 10
4
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3
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2.4k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.6 years ago • updated 2.5 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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1.9k
views
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
reply
3.6k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.6 years ago merv ▴ 150
0
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0
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1.5k
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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
views
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
0
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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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5.8k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.1 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 3.0 years ago by ▴ 780 • written 3.0 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
3.1 years ago msn ▴ 10
0
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1
reply
931
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.2 years ago by 68k • written 3.2 years ago by • 0
2
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2
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1.5k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.3 years ago by ★ 4.8k • written 3.3 years ago by ▴ 40
0
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0
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863
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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
3.4 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
3.4 years ago enricoferrero ▴ 680
0
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1
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3.5k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.6 years ago by ★ 4.8k • written 3.6 years ago by • 0
2
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5
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6.3k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 3.9 years ago by ▴ 60 • written 3.9 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 • updated 4.1 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 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 10
4
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5
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3.3k
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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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1.7k
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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
4.3 years ago achaillon • 0
0
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2
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1.8k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.3 years ago jirkanov • 0
2
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2
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2.7k
views
Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
4.3 years ago lirongrossmann ▴ 50
0
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1
reply
1.1k
views
improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 4.4 years ago by ★ 28k • written 4.4 years ago by ▴ 50
50 results • Page 1 of 1
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Comment: DESeq2 - human data, weird results, troubleshooting by bd2000 ▴ 30
I didn't include all of my code the post would be too long. Here's a link to my GitHub if anyone would like to see the full code: [Full Rst…
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin by James W. MacDonald 68k
The simple answer is that the within-group variability is much higher for the first gene as compared to the second. The Wald statistic is j…
Comment: DESeq: Gene is not flagged as differentially expressed despite count data showin by ATpoint ★ 4.8k
> since there doesn't seem to be as much count variability, No? Your CD45 samples range on normalized scale from 2 to 3255. That's 3 orde…
Comment: Ensembl site unresponsive via biomaRt by darylruiz6545 • 0
Thank you so much for sharing the link.
Comment: compute_fasta_digest does not match Salmon index hash by Alex • 0
I use the `fastaDigest` tool from [COMBINE-lab/fastaDigest](https://github.com/COMBINE-lab/FastaDigest/), which has the function `compute_f…
Votes
Answer: DESeq: Gene is not flagged as differentially expressed despite count data showin
Two EPIC Methylation Array Analysis Questions
How to get DMR for Infinium methylation EPIC v2
A: GEOquery Fails to Download Series Matrix File
Comment: Gene IDs conversion between Ensembl and NCBI nomenclature for non-model species
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