Showing : singleCellExperiment • reset
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 6 hours ago by ★ 4.0k • written 5 weeks ago by • 0
0
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1
reply
180
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
10 weeks ago • updated 9 weeks ago Francesco Silvestro • 0
0
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0
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127
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
10 weeks ago Ludwig Geistlinger ▴ 70
3
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9
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4.5k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 10 days ago by • 0 • written 4 months ago by ▴ 10
4
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17
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5.7k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 5 months ago by ★ 5.0k • written 6 months ago by ▴ 10
1
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3
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1.2k
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
5 months ago Konstantinos Yeles ▴ 90
3
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2
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759
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 8 months ago by ▴ 40 • written 9 months ago by • 0
0
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0
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352
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
12 months ago Ibrahim • 0
0
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0
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551
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
13 months ago info ▴ 10
2
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2
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822
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 14 months ago by ▴ 10
2
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1
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2.1k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 15 months ago by ★ 29k • written 15 months ago by • 0
0
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1
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632
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T cell subtype annotation
SingleCellExperiment
updated 16 months ago by 68k • written 16 months ago by • 0
0
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1
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3.2k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 16 months ago by • 0 • written 16 months ago by • 0
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0
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
16 months ago Stefano Mangiola ▴ 40
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4
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1.2k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
17 months ago vohara4 • 0
4
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1
reply
1.8k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 21 months ago by 68k • written 21 months ago by ▴ 20
4
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6
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1.5k
views
Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
22 months ago • updated 21 months ago Dario Strbenac ★ 1.6k
0
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0
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525
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rpk per cell saved in SCE object.
SingleCellExperiment
22 months ago JalapenoCornbread • 0
1
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2
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1.8k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
23 months ago elgomez • 0
0
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10
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3.7k
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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 23 months ago by • 0
0
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1
reply
1.0k
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.1 years ago by • 0
2
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5
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1.8k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.3 years ago • updated 2.2 years ago duez.tolga • 0
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2
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2.0k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.4 years ago Matvii Mykhailichenko • 0
0
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2
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1.8k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.4 years ago Lluís Revilla Sancho ▴ 760
1
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3
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3.8k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.5 years ago mollyab12 • 0
0
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1
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2.1k
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Rename colData column
SingleCellExperiment colData rename
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by ▴ 10
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3
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2.5k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.8 years ago by ▴ 40 • written 6.8 years ago by ▴ 10
4
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3
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2.8k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.2 years ago • updated 3.1 years ago merv ▴ 150
2
votes
4
replies
2.1k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 20
2
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4
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1.6k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.2 years ago Romina • 0
1
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1
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2.4k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.2 years ago by ▴ 760 • written 3.2 years ago by ▴ 150
5
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1
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4.0k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.2 years ago merv ▴ 150
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0
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1.8k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.2 years ago merv ▴ 150
4
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3
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2.6k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.3 years ago by 68k • written 3.3 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 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
2
votes
5
replies
6.4k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.7 years ago by • 0 • written 3.5 years ago by ▴ 10
2
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1
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1.9k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.6 years ago by ▴ 780 • written 3.6 years ago by • 0
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2
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1.5k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.7 years ago msn ▴ 10
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1
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1.1k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
2
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2
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1.7k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.9 years ago by ★ 5.0k • written 3.9 years ago by ▴ 40
0
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0
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1.0k
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.9 years ago Núria • 0
1
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2
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1.3k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.0 years ago Fatima • 0
3
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3
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2.6k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.0 years ago enricoferrero ▴ 680
0
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1
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3.8k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by • 0
2
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5
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6.9k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.5 years ago by ▴ 60 • written 4.5 years ago by ▴ 20
2
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3
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2.0k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.8 years ago by ▴ 160 • written 4.8 years ago by • 0
3
votes
2
replies
3.4k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.8 years ago • updated 4.7 years ago camerond • 0
0
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7
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3.1k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.8 years ago • updated 4.7 years ago bge • 0
1
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3
replies
2.5k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.8 years ago by ★ 29k • written 4.8 years ago by ▴ 10
4
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5
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3.8k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.8 years ago by ★ 29k • written 4.8 years ago by ▴ 680
93 results • Page 1 of 2
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Comment: Ensembl 115 has been released! by eja.gsssssswwse.r.m • 0
Keeping up with Ensembls latest release ensures access to cutting-edge genomic information. For those balancing research and leisure, a mob…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
Votes
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Suppress warning in RHDF5 write
Answer: Suppress warning in RHDF5 write
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