Showing : SingleCellExperiment • reset
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Streamlining the computing time for MiloDE p-value correction in large dataset?
SingleCellExperiment edgeR miloR Bioconductor
updated 5 days ago by ★ 5.0k • written 8 days ago by • 0
0
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1
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141
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Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
5 weeks ago Francesco Silvestro • 0
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98
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
5 weeks ago Ludwig Geistlinger ▴ 70
3
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1
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4.0k
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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 ★ 29k • written 3 months ago by ▴ 10
4
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17
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5.5k
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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
4 months ago Konstantinos Yeles ▴ 90
3
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2
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674
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 7 months ago by ▴ 40 • written 8 months ago by • 0
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328
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
11 months ago Ibrahim • 0
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0
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514
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
12 months ago info ▴ 10
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2
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779
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 13 months ago by ▴ 10
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1
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2.0k
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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
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1
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535
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T cell subtype annotation
SingleCellExperiment
updated 15 months ago by 68k • written 15 months ago by • 0
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1
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3.1k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 15 months ago by • 0 • written 15 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
15 months ago Stefano Mangiola ▴ 40
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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 20 months ago by 68k • written 20 months ago by ▴ 20
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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 • updated 20 months ago Dario Strbenac ★ 1.6k
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502
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rpk per cell saved in SCE object.
SingleCellExperiment
20 months ago JalapenoCornbread • 0
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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
22 months ago elgomez • 0
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10
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3.6k
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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 22 months ago by • 0
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1.0k
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.0 years ago by • 0
2
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5
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1.7k
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
2.2 years ago duez.tolga • 0
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2
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1.9k
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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
2.3 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 • updated 2.4 years ago mollyab12 • 0
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1
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2.0k
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Rename colData column
SingleCellExperiment colData rename
updated 2.6 years ago by ▴ 780 • written 2.6 years ago by ▴ 10
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3
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2.4k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 2.7 years ago by ▴ 40 • written 6.7 years ago by ▴ 10
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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 • updated 3.0 years ago merv ▴ 150
2
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4
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2.0k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 11 weeks ago by • 0 • written 3.1 years ago by ▴ 20
2
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4
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1.6k
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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 3.1 years ago by ▴ 760 • written 3.1 years ago by ▴ 150
5
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1
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3.9k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.1 years ago merv ▴ 150
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1.7k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.1 years ago merv ▴ 150
4
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3
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2.6k
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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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6.3k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.6 years ago by • 0 • written 3.5 years ago by ▴ 10
2
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1
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1.8k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.5 years ago by ▴ 780 • written 3.5 years ago by • 0
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2
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1.4k
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
3.6 years ago msn ▴ 10
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1
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1.0k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.7 years ago by 68k • written 3.7 years ago by • 0
2
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2
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1.7k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.8 years ago by ★ 5.0k • written 3.8 years ago by ▴ 40
0
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0
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974
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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
3.9 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 • updated 3.9 years ago enricoferrero ▴ 680
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1
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3.8k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.1 years ago by ★ 5.0k • written 4.1 years ago by • 0
2
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5
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6.8k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.4 years ago by ▴ 60 • written 4.4 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
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7
replies
3.1k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.7 years ago • updated 4.6 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 4.7 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: Help with defining groups by Phinney, Brett ▴ 10
I got it working , thank you!!!
Comment: Check removeBatchEffect effectiveness by massimo • 0
I would kindly ask for additional support. When not including the design_timepoint argument in removeBatchEffect and thus keeping the inter…
Comment: Error Loading Experiment from SimBenchData Package by ksankaran • 0
Aha, that was it! The object was class Seurat, but I didn't have it installed. After installing, everything works as expected.
Comment: Streamlining the computing time for MiloDE p-value correction in large dataset? by ATpoint ★ 5.0k
Is a method that is so computationally expensive really beneficial and necessary? You seem to have biological replication, don't you, so ps…
Answer: NA values for DESeq2 p-values and adjusted p-values using large sample sizes by ATpoint ★ 5.0k
Outliers without replacement, independent filtering or all-zero counts for that gene. That's the three options that trigger NAs https://bio…
Votes
Comment: Check removeBatchEffect effectiveness
Gene expression associated with continuous (quantitative) traits (Limma/edgeR/correlation)
Answer: Error Loading Experiment from SimBenchData Package
Comment: incomplete imputation of missing values with LEA impute() function
Answer: Expected memory usage for analyzing large single-cell seq datasets (> 450,000 ce
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