Showing : singlecellexperiment • reset
0
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3
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2.5k
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PCA outliers cleaning
scRNAseq Pipeline Seurat SingleCellExperiment
written 6.3 years ago by ▴ 10
0
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1
reply
402
views
Length of 'dimnames' [1] not equal to array extent
SingleCellExperiment singlecelle scRNAseq
updated 3 months ago by ★ 4.0k • written 6 months ago by • 0
1
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2
replies
569
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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
0
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0
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214
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
6 months ago Ludwig Geistlinger ▴ 80
3
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9
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5.0k
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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 • 0 • written 7 months ago by ▴ 10
4
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17
replies
6.8k
views
How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 8 months ago by ★ 5.0k • written 9 months ago by ▴ 10
1
vote
3
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1.4k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
9 months ago Konstantinos Yeles ▴ 90
3
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2
replies
864
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 12 months ago by ▴ 40 • written 13 months ago by • 0
0
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0
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460
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
16 months ago Ibrahim • 0
0
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0
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637
views
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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961
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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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3.0k
views
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
reply
756
views
T cell subtype annotation
SingleCellExperiment
updated 19 months ago by 68k • written 19 months ago by • 0
0
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1
reply
5.4k
views
converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 20 months ago by • 0 • written 20 months ago by • 0
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0
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1.1k
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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
0
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4
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1.4k
views
Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
20 months ago vohara4 • 0
4
votes
1
reply
2.1k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 2.1 years ago by 68k • written 2.1 years ago by ▴ 20
4
votes
6
replies
1.7k
views
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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579
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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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2.1k
views
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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4.0k
views
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
reply
1.2k
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 2.4 years ago by • 0
2
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5
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2.0k
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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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2.2k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.7 years ago Matvii Mykhailichenko • 0
0
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2
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2.1k
views
runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
2.7 years ago Lluís Revilla Sancho ▴ 760
1
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3
replies
4.1k
views
Remove certain highly expressing cells from a SCE
SingleCellExperiment
2.8 years ago mollyab12 • 0
0
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1
reply
2.3k
views
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
replies
2.6k
views
How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 3.1 years ago by ▴ 40 • written 7.1 years ago by ▴ 10
4
votes
3
replies
3.0k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.5 years ago • updated 3.4 years ago merv ▴ 150
2
votes
4
replies
2.2k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 7 months ago by • 0 • written 3.5 years ago by ▴ 20
2
votes
4
replies
1.8k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.5 years ago Romina • 0
1
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1
reply
2.7k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.5 years ago by ▴ 760 • written 3.5 years ago by ▴ 150
5
votes
1
reply
4.2k
views
How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
3.5 years ago merv ▴ 150
0
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0
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2.1k
views
Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
3.5 years ago merv ▴ 150
4
votes
3
replies
2.9k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.6 years ago by 68k • written 3.6 years ago by ▴ 10
0
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1
reply
1.6k
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 3.7 years ago by ★ 5.0k • written 3.7 years ago by • 0
2
votes
5
replies
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
reply
2.1k
views
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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1.7k
views
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
reply
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
votes
2
replies
1.8k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 4.2 years ago by ★ 5.0k • written 4.2 years ago by ▴ 40
0
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0
replies
1.1k
views
scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
4.2 years ago Núria • 0
1
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2
replies
1.5k
views
Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
4.3 years ago Fatima • 0
3
votes
3
replies
2.9k
views
Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
4.3 years ago enricoferrero ▴ 680
0
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1
reply
4.0k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.5 years ago by ★ 5.0k • written 4.5 years ago by • 0
2
votes
5
replies
7.6k
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
votes
3
replies
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
votes
2
replies
3.8k
views
Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
5.1 years ago • updated 5.0 years ago camerond • 0
0
votes
7
replies
3.4k
views
SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
5.1 years ago • updated 5.0 years ago bge • 0
1
vote
3
replies
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
93 results • Page 1 of 2
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Comment: Reproducibility of code in various Bioconductor versions by Gordon Smyth 53k
SNPlocs.Hsapiens.dbSNP155.GRCh38 is available for download from the same location as always. It has not changed since Bioc 3.20: Presumabl…
Comment: Changing multiple display parameters of a specific exon in GeneRegionTrack by a2a2hd42aa • 0
Similarly, for structural complexity in the [He777 Game][1] APK, having precise control over every detail is what makes a high-performance …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by strawberry3 • 0
Hi, thank you all for the advice. Using James's advice, I managed to install SNPlocs.Hsapiens.dbSNP155.GRCh38, but it took almost half an …
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by James W. MacDonald 68k
As Robert and ATpoint have mentioned, you need to allow more time to download a large file like this. ``` > options(timeout = 5e5) > l…
Answer: Issue loading and downloading Bioconductor 3.22 packages after update by Robert Castelo ★ 3.4k
Hi, the package you refer to is not called `SNPlocs.HSapiens.dbSNP155.GRCh38`, but `SNPlocs.Hsapiens.dbSNP155.GRCh38`, note the lowercase l…
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Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Issue loading and downloading Bioconductor 3.22 packages after update
Comment: Issue loading and downloading Bioconductor 3.22 packages after update
Answer: Question on processing compound protein groups in limpa
Answer: Correct usage of limpa for protein input
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