Showing : SingleCellExperiment • reset
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 29 days ago by ★ 4.0k • written 3 months ago by • 0
1
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2
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446
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 5 weeks ago by ★ 4.0k • written 11 weeks ago by • 0
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156
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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 7 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
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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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801
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 9 months ago by ▴ 40 • written 11 months ago by • 0
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379
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
14 months ago Ibrahim • 0
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0
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578
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
14 months ago info ▴ 10
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2
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869
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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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700
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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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3.5k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 17 months ago by • 0 • written 18 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
18 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
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 23 months ago by 68k • written 23 months ago by ▴ 20
4
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6
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1.6k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
23 months ago Dario Strbenac ★ 1.6k
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0
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543
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rpk per cell saved in SCE object.
SingleCellExperiment
23 months ago JalapenoCornbread • 0
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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
2.0 years 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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1.1k
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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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1.9k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.4 years ago • updated 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
2.5 years ago Matvii Mykhailichenko • 0
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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2.9k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.3 years ago • updated 3.2 years ago merv ▴ 150
2
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4
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2.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 4 months ago by • 0 • written 3.3 years ago by ▴ 20
2
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4
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1.7k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.3 years ago Romina • 0
1
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1
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2.4k
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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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4.1k
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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
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.4 years ago by 68k • written 3.4 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 3.5 years ago by ★ 5.0k • written 3.5 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
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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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2.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.2 years ago • updated 4.1 years ago enricoferrero ▴ 680
0
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1
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3.9k
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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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7.0k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.6 years ago by ▴ 60 • written 4.6 years ago by ▴ 20
2
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3
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2.0k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.9 years ago by ▴ 160 • written 4.9 years ago by • 0
3
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2
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3.5k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.9 years ago camerond • 0
0
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7
replies
3.2k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.9 years ago • updated 4.8 years ago bge • 0
1
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3
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2.6k
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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
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3.9k
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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
Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
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…
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
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