Showing : singlecellexperiment • reset
4
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17
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5.2k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 4 weeks ago by ★ 4.9k • written 9 weeks ago by ▴ 10
1
vote
3
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1.0k
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
6 weeks ago • updated 5 weeks ago Konstantinos Yeles ▴ 90
3
votes
2
replies
590
views
SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 4 months ago by ▴ 40 • written 5 months ago by • 0
0
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0
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247
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
8 months ago Ibrahim • 0
0
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0
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410
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
9 months ago info ▴ 10
2
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2
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686
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 10 months ago by ▴ 10
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1
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1.9k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 11 months ago by ★ 28k • written 11 months ago by • 0
0
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1
reply
480
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T cell subtype annotation
SingleCellExperiment
updated 11 months ago by 68k • written 11 months ago by • 0
0
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1
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2.8k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 12 months ago by • 0 • written 12 months ago by • 0
0
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0
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816
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
12 months ago Stefano Mangiola ▴ 40
0
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4
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956
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
13 months ago • updated 12 months ago vohara4 • 0
4
votes
1
reply
1.7k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 17 months ago by 68k • written 17 months ago by ▴ 20
4
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6
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1.4k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
17 months ago Dario Strbenac ★ 1.6k
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0
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454
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rpk per cell saved in SCE object.
SingleCellExperiment
17 months ago JalapenoCornbread • 0
1
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2
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1.7k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
19 months ago elgomez • 0
0
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8
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3.3k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
updated 11 weeks ago by • 0 • written 19 months ago by • 0
0
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1
reply
957
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 21 months ago by • 0
2
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5
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1.6k
views
Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
23 months ago duez.tolga • 0
0
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2
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1.9k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.0 years ago Matvii Mykhailichenko • 0
0
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2
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1.7k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.0 years ago Lluís Revilla Sancho ▴ 760
1
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3
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3.7k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.2 years ago mollyab12 • 0
0
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1
reply
1.9k
views
Rename colData column
SingleCellExperiment colData rename
updated 2.4 years ago by ▴ 780 • written 2.4 years ago by ▴ 10
2
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3
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2.4k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.5 years ago by ▴ 40 • written 6.4 years ago by ▴ 10
4
votes
3
replies
2.6k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
2.8 years ago merv ▴ 150
2
votes
3
replies
1.8k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 24 days ago by • 0 • written 2.8 years ago by ▴ 20
2
votes
4
replies
1.4k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.8 years ago Romina • 0
1
vote
1
reply
2.2k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 150
5
votes
1
reply
3.8k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
2.8 years ago merv ▴ 150
0
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0
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1.6k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
2.8 years ago merv ▴ 150
4
votes
3
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2.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 10
0
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1
reply
1.5k
views
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 3.0 years ago by ★ 4.9k • written 3.0 years ago by • 0
2
votes
5
replies
6.2k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.4 years ago by • 0 • written 3.2 years ago by ▴ 10
2
votes
1
reply
1.7k
views
Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.3 years ago by ▴ 780 • written 3.3 years ago by • 0
1
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2
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1.4k
views
How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.4 years ago msn ▴ 10
0
votes
1
reply
990
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.5 years ago by 68k • written 3.5 years ago by • 0
2
votes
2
replies
1.6k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.6 years ago by ★ 4.9k • written 3.6 years ago by ▴ 40
0
votes
0
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912
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.6 years ago Núria • 0
1
vote
2
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1.2k
views
Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
3.7 years ago • updated 3.6 years ago Fatima • 0
3
votes
3
replies
2.4k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.7 years ago enricoferrero ▴ 680
0
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1
reply
3.7k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.9 years ago by ★ 4.9k • written 3.9 years ago by • 0
2
votes
5
replies
6.7k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.1 years ago by ▴ 60 • written 4.2 years ago by ▴ 20
2
votes
3
replies
1.9k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.4 years ago by ▴ 160 • written 4.4 years ago by • 0
3
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2
replies
3.3k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.4 years ago camerond • 0
0
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7
replies
3.0k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.4 years ago bge • 0
1
vote
3
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2.4k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 10
4
votes
5
replies
3.6k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.5 years ago by ★ 28k • written 4.5 years ago by ▴ 680
0
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2
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1.8k
views
from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
4.5 years ago achaillon • 0
1
vote
3
replies
1.5k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.5 years ago by ▴ 70 • written 4.6 years ago by • 0
2
votes
3
replies
2.2k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.6 years ago • updated 4.5 years ago achaillon • 0
0
votes
2
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1.9k
views
Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
4.6 years ago jirkanov • 0
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Answer: Regarding the issue of background genes in enrichment analysis by ATpoint ★ 4.9k
It should imo be the genes that were eligable to yield a "significant" result in your analysis. So, if you test set is derived from differe…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by Gordon Smyth 52k
> How do these logFC values compare to standard effect sizes derived using a basic regression model like lm()? Exactly the same. Both soft…
Comment: Applying lmFit(), eBayes() and topTable() for modeling associations between NMR- by anni • 0
Ok, thanks! I have just a couple more questions: 1. Based on the [limma User's Guide][1], for binary predictors like overweight, I have i…
Comment: Online workshop "Working with ChatGPT in R" 2023-03-09 by tnaru607 • 0
Thanks for sharing your workflow and benchmarking approach - very informative! I've been experimenting with AI-assisted tools recently, es…
Comment: minfi latest update for EPIC V2 chip by UlyssesHenson • 0
These provide updated manifests and annotations aligned with the latest genome build (hg38) and probe content for the EPIC V2 array. [itali…
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Answer: I would like to perform differential expression analysis of lncRNAs using DESeq2
I would like to perform differential expression analysis of lncRNAs using DESeq2 and edgeR.
Answer: ExperimentHub full metadata
Answer: AnnotationHub/ExperimentHub resources backup
Answer: ExperimentHub full metadata
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