Showing : SingleCellExperiment • reset
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
written 6.3 years ago by ▴ 10
0
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1
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380
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 12 weeks ago by ★ 4.0k • written 5 months ago by • 0
1
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2
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531
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 3 months ago by ★ 4.0k • written 4 months ago by • 0
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194
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
5 months ago Ludwig Geistlinger ▴ 80
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9
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4.9k
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 3 months ago by • 0 • written 7 months ago by ▴ 10
4
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17
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6.5k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 8 months ago by ★ 5.0k • written 9 months ago by ▴ 10
1
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3
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1.3k
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
8 months ago Konstantinos Yeles ▴ 90
3
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2
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856
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 11 months ago by ▴ 40 • written 13 months ago by • 0
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449
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
15 months ago Ibrahim • 0
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0
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625
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
16 months ago info ▴ 10
2
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2
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946
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 17 months ago by ▴ 10
2
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1
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2.8k
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Expected memory usage for analyzing large single-cell seq datasets (> 450,000 cells)?
BigData Clustering memory SingleCellExperiment edgeR
updated 18 months ago by ★ 29k • written 18 months ago by • 0
0
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1
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747
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T cell subtype annotation
SingleCellExperiment
updated 19 months ago by 68k • written 19 months ago by • 0
0
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1
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5.1k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 19 months ago by • 0 • written 20 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
20 months ago Stefano Mangiola ▴ 40
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4
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1.4k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 months ago vohara4 • 0
4
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1
reply
2.1k
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 2.0 years ago by 68k • written 2.0 years ago by ▴ 20
4
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6
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1.7k
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
2.1 years ago Dario Strbenac ★ 1.6k
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0
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575
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rpk per cell saved in SCE object.
SingleCellExperiment
2.1 years ago JalapenoCornbread • 0
1
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2
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2.0k
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
2.2 years ago elgomez • 0
0
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10
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3.9k
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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 2.2 years ago by • 0
0
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1
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1.2k
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.3 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
2.5 years ago duez.tolga • 0
0
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2
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2.1k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.6 years ago Matvii Mykhailichenko • 0
0
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2
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2.0k
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.6 years ago Lluís Revilla Sancho ▴ 760
1
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3
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4.1k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.8 years ago mollyab12 • 0
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1
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2.2k
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Rename colData column
SingleCellExperiment colData rename
updated 3.0 years ago by ▴ 780 • written 3.0 years ago by ▴ 10
2
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3
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2.6k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 3.1 years ago by ▴ 40 • written 7.0 years ago by ▴ 10
4
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3
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3.0k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago merv ▴ 150
2
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4
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2.2k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
2
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4
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1.8k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.4 years ago Romina • 0
1
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1
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2.7k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.4 years ago by ▴ 760 • written 3.4 years ago by ▴ 150
5
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1
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4.2k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago merv ▴ 150
0
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0
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2.0k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.4 years ago merv ▴ 150
4
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3
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2.8k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.5 years ago by 68k • written 3.5 years ago by ▴ 10
0
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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 3.6 years ago by ★ 5.0k • written 3.6 years ago by • 0
2
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5
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6.7k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 3.0 years ago by • 0 • written 3.8 years ago by ▴ 10
2
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1
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2.1k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.9 years ago by ▴ 780 • written 3.9 years ago by • 0
1
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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
4.0 years ago msn ▴ 10
0
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1
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1.2k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 4.1 years ago by 68k • written 4.1 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 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 40
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0
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1.1k
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
4.2 years ago Núria • 0
1
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2
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1.5k
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.3 years ago • updated 4.2 years ago Fatima • 0
3
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3
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2.8k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.3 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 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
2
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5
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7.5k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.7 years ago by ▴ 60 • written 4.8 years ago by ▴ 20
2
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3
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2.1k
views
how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 5.0 years ago by ▴ 160 • written 5.0 years ago by • 0
3
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2
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3.7k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
5.0 years ago camerond • 0
0
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7
replies
3.4k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
5.0 years ago bge • 0
1
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3
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2.7k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 10
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Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you so much for your help! will try to proceed with the suggestion
Comment: GSEA in R/Bioconductor course by a2a2haa • 0
Academic researchers often share their breakthroughs and course updates through visual stories, making it essential to have tools that pres…
Comment: Bulk RNAseq analysis for by Mariami • 0
Thank you for the explanation. I understand, although at the moment we are limited in our ability to increase N. My concern came from the o…
Answer: Bulk RNAseq analysis for by Gordon Smyth 53k
All three packages allow paired comparisons, where the clone is the "pair". limma moreover allows mixed models (just run `voomLmFit` with `…
Comment: Announcing a New Journal - Bioinformatics Methods and Applications - Now Open fo by a2a2haa • 0
By promoting reproducible analysis, the scientific community can better understand the precise mechanisms that make [Hydrogen inhalation sa…
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Comment: Are transformed values from rlog /vst log2 normalized counts?
Are transformed values from rlog /vst log2 normalized counts?
Answer: Bulk RNAseq analysis for
Answer: DiffBind differential analysis
Answer: Limma-voom sample weights and impact on DEG numbers
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