Showing : singlecellexperiment • reset
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 19 days ago by ★ 4.0k • written 3 months ago by • 0
1
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2
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434
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 4 weeks ago by ★ 4.0k • written 9 weeks ago by • 0
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149
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
3 months ago Ludwig Geistlinger ▴ 70
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9
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4.6k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 5 weeks ago by • 0 • written 5 months ago by ▴ 10
4
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17
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5.8k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 6 months ago by ★ 5.0k • written 7 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
6 months ago Konstantinos Yeles ▴ 90
3
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2
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790
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 9 months ago by ▴ 40 • written 10 months ago by • 0
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372
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
13 months ago Ibrahim • 0
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0
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571
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
14 months ago info ▴ 10
2
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2
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859
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 15 months ago by ▴ 10
2
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1
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2.2k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 16 months ago by ★ 29k • written 16 months ago by • 0
0
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1
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692
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T cell subtype annotation
SingleCellExperiment
updated 17 months ago by 68k • written 17 months ago by • 0
0
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1
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3.4k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 17 months ago by • 0 • written 17 months ago by • 0
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992
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
17 months ago Stefano Mangiola ▴ 40
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4
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1.3k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
18 months ago vohara4 • 0
4
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1
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1.9k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 22 months ago by 68k • written 22 months ago by ▴ 20
4
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6
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1.5k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
23 months ago • updated 22 months ago Dario Strbenac ★ 1.6k
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540
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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
24 months ago elgomez • 0
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10
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3.8k
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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 2.0 years ago by • 0
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1
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1.1k
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.2 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 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
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2
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1.9k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.5 years ago Lluís Revilla Sancho ▴ 760
1
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3
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3.9k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.6 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 2.8 years ago by ▴ 780 • written 2.8 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 2.9 years ago by ▴ 40 • written 6.9 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 merv ▴ 150
2
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4
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2.1k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 4 months ago by • 0 • written 3.2 years ago by ▴ 20
2
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4
replies
1.7k
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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 3.3 years ago by ▴ 760 • written 3.3 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
3.3 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
3.3 years ago merv ▴ 150
4
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3
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2.7k
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
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5
replies
6.5k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.8 years ago by • 0 • written 3.6 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 3.7 years ago by ▴ 780 • written 3.7 years ago by • 0
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2
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1.6k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.8 years ago msn ▴ 10
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1
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1.1k
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
2
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2
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1.8k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.0 years ago by ★ 5.0k • written 4.0 years ago by ▴ 40
0
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0
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1.0k
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
4.0 years ago Núria • 0
1
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2
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1.4k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.1 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
4.1 years ago enricoferrero ▴ 680
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1
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3.8k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.3 years ago by ★ 5.0k • written 4.3 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 4.6 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
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2
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3.5k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.8 years ago camerond • 0
0
votes
7
replies
3.2k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.9 years ago • updated 4.8 years ago bge • 0
1
vote
3
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2.6k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 10
4
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5
replies
3.9k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 680
93 results • Page 1 of 2
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Awards • All
Popular Question to Gordon Smyth 53k
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
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