Showing : SingleCellExperiment • reset
3
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Best practice for handling large data (matrix with >2^31-1 non-zero elements) in SingleCellExperiment?
SingleCellExperiment
updated 6 weeks ago by ★ 29k • written 7 weeks ago by ▴ 10
4
votes
17
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5.3k
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How to load scRNA-seq data from GEO
SingleCellExperiment GEO
updated 12 weeks ago by ★ 4.9k • written 3 months ago by ▴ 10
1
vote
3
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1.1k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
3 months ago Konstantinos Yeles ▴ 90
3
votes
2
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637
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SingleCellExperiment convenience function for metadata+expression?
SpatialExperiment SingleCellExperiment SpatialFeatureExperiment
updated 6 months ago by ▴ 40 • written 7 months ago by • 0
0
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0
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282
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cbind for multiple SpatialExperiment takes so much time
SpatialExperiment SingleCellExperiment
10 months ago Ibrahim • 0
0
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0
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473
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News: Single-cell RNA-seq analysis with R/Bioconductor (online course)
SingleCellExperiment SingleCell
10 months ago info ▴ 10
2
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2
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726
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Should tSNE from biol. replicates look alike?
scRNAseq SingleCellExperiment batchelor
written 11 months ago by ▴ 10
1
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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 12 months ago by ★ 29k • written 12 months ago by • 0
0
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1
reply
516
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T cell subtype annotation
SingleCellExperiment
updated 13 months ago by 68k • written 13 months ago by • 0
0
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1
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3.0k
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converting Seurat V5 with BPcells matrix to SingleCellExperiment
SeuratV5 SingleCellExperiment BPCells SingleCellExper
updated 14 months ago by • 0 • written 14 months ago by • 0
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0
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Job: Postdoc+PhD position: Spatial & Single-Cell Computational Immunogenomics for Cancer Diagnosis
JobPosting CuratedAtlasQueryR MoleculeExperiment SingleCellExperiment SpatialExperiment
14 months ago Stefano Mangiola ▴ 40
0
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4
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1.0k
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Single Cell Experiment : Differential Expression "List of length 0" - Help!
DifferentialExpression scran scater SingleCellExperiment edgeR
14 months ago vohara4 • 0
4
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1
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1.8k
views
When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 19 months ago by 68k • written 19 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
19 months ago Dario Strbenac ★ 1.6k
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0
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481
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rpk per cell saved in SCE object.
SingleCellExperiment
19 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
20 months ago elgomez • 0
0
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9
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3.5k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 21 months ago by • 0
0
votes
1
reply
987
views
Subsetting cells from a single cell experiment
SingleCellExperiment
written 22 months 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
2.1 years ago • updated 2.0 years ago duez.tolga • 0
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
2.2 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
2.2 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
2.3 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 2.5 years ago by ▴ 780 • written 2.5 years ago by ▴ 10
2
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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 2.6 years ago by ▴ 40 • written 6.6 years ago by ▴ 10
4
votes
3
replies
2.7k
views
Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
3.0 years ago • updated 2.9 years ago merv ▴ 150
2
votes
4
replies
1.9k
views
How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 5 weeks ago by • 0 • written 3.0 years ago by ▴ 20
2
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4
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1.5k
views
Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.0 years ago Romina • 0
1
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1
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2.3k
views
Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 3.0 years ago by ▴ 760 • written 3.0 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
3.0 years ago merv ▴ 150
0
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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
3.0 years ago merv ▴ 150
4
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3
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2.5k
views
SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 3.1 years ago by 68k • written 3.1 years ago by ▴ 10
0
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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 3.2 years ago by ★ 4.9k • written 3.2 years ago by • 0
2
votes
5
replies
6.3k
views
Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 2.5 years ago by • 0 • written 3.3 years ago by ▴ 10
2
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1
reply
1.8k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 3.4 years ago by ▴ 780 • written 3.4 years ago by • 0
1
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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
3.5 years ago msn ▴ 10
0
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1
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1.0k
views
Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 3.6 years ago by 68k • written 3.6 years ago by • 0
2
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2
replies
1.6k
views
velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 3.7 years ago by ★ 4.9k • written 3.7 years ago by ▴ 40
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0
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944
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
3.7 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
3.8 years ago Fatima • 0
3
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3
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2.4k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
3.8 years ago enricoferrero ▴ 680
0
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1
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3.7k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.0 years ago by ★ 4.9k • written 4.0 years ago by • 0
2
votes
5
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6.8k
views
Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 4.3 years ago by ▴ 60 • written 4.3 years ago by ▴ 20
2
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3
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1.9k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 4.6 years ago by ▴ 160 • written 4.6 years ago by • 0
3
votes
2
replies
3.4k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
4.6 years ago • updated 4.5 years ago camerond • 0
0
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7
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3.0k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
4.6 years ago • updated 4.5 years ago bge • 0
1
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3
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2.4k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.6 years ago by ★ 29k • written 4.6 years ago by ▴ 10
4
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5
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3.6k
views
scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 4.6 years ago by ★ 29k • written 4.6 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
4.7 years ago achaillon • 0
1
vote
3
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1.6k
views
singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 4.7 years ago by ▴ 70 • written 4.7 years ago by • 0
2
votes
3
replies
2.3k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.7 years ago achaillon • 0
90 results • Page 1 of 2
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Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea by James W. MacDonald 68k
Your approach 1 is a bad idea. Subtracting the gene counts won't do what you want to do. I would personally check to see if there is any…
Comment: Can NanoString data be analyzed using DESeq2? by James W. MacDonald 68k
You can always discard, although you can also retain them to check for unexpected differences.
Comment: DESeq2 on NanoString Data by Michael Love 43k
Yes, if I discern a batch from EDA including looking at PCs, sample correlations, etc. It is close to SVA, we discuss both in the workflow…
Comment: DESeq2 on NanoString Data by thkapell ▴ 10
Thanks Michael. To this end, do you routinely use RUV or only when you detect a batch? It looks like it works in a similar fashion to SVA w…
Comment: Can NanoString data be analyzed using DESeq2? by thkapell ▴ 10
Thank you. I agree with your thoughts about the similarities of NanoString with RNA-seq. NanoString though, also has positive, negative pro…
Votes
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Answer: How to account for solvent controls in DESeq2 when comparing follicular vs lutea
Comment: Using DESeq2 on single cell RNA Seq data of same cell type but different conditi
Can NanoString data be analyzed using DESeq2?
Comment: Are voomByGroup and voomLmFit compatible?
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