Showing : SingleCellExperiment • reset
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 25 days ago by ★ 5.0k • written 29 days ago by • 0
0
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1
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162
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
8 weeks ago • updated 7 weeks ago Francesco Silvestro • 0
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0
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119
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
8 weeks ago Ludwig Geistlinger ▴ 70
3
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9
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4.4k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 18 hours ago by • 0 • written 3 months ago by ▴ 10
4
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17
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5.6k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 4 months ago by ★ 5.0k • written 5 months ago by ▴ 10
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3
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1.1k
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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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713
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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
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0
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342
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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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534
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
12 months ago info ▴ 10
2
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2
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808
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 13 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 14 months ago by ★ 29k • written 14 months ago by • 0
0
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1
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570
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T cell subtype annotation
SingleCellExperiment
updated 15 months ago by 68k • written 15 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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948
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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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1.1k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
16 months ago vohara4 • 0
4
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1
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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
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
21 months ago Dario Strbenac ★ 1.6k
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0
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513
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rpk per cell saved in SCE object.
SingleCellExperiment
21 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
22 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
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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
2.2 years ago duez.tolga • 0
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
2.3 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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2.0k
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Rename colData column
SingleCellExperiment colData rename
updated 2.7 years ago by ▴ 780 • written 2.7 years ago by ▴ 10
2
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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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2.7k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.1 years ago merv ▴ 150
2
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4
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2.0k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 3 months ago by • 0 • written 3.1 years ago by ▴ 20
2
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4
replies
1.6k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.1 years ago Romina • 0
1
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1
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2.3k
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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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1.7k
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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 3.2 years ago by 68k • written 3.2 years ago by ▴ 10
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1
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1.5k
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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 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
2
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5
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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
1
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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
0
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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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985
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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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2.5k
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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 4.4 years ago by ▴ 60 • written 4.5 years ago by ▴ 20
2
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3
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1.9k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.7 years ago by ▴ 160 • written 4.7 years ago by • 0
3
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2
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3.4k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.7 years ago camerond • 0
0
votes
7
replies
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
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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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3.7k
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
Recent ...
Replies
Comment: deseq2 filter the low counts by Michael Love 43k
Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering
Comment: deseq2 filter the low counts by empty_mt • 0
Hi Michael, My matrix consists of 36 samples from 6 treatments (6 samples/ treatment), whether I adjust prefiltering parameters or not, in…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
That works. I didn't realize what you said about HDF5 files. We always keep those and archive the MTX files. I'm able to read in the file…
Comment: DESeq2 interactions by Michael Love 43k
GPT even v4 gives pretty good answers to DESeq2 questions that are similar to those already posted on the support site. I've also noticed …
Answer: Important: Bioconductor Release 3.22 Delayed by shepherl 4.2k
We will continue with the release on Thursday October 30th. We have shifted one day as originally planned. Thank you
Votes
Answer: DESeq2 interactions
Answer: Important: Bioconductor Release 3.22 Delayed
A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
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