Showing : SingleCellExperiment • reset
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When should I correct for batch effects
BatchEffect SingleCellExperiment
updated 3 months ago by 65k • written 3 months ago by • 0
4
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6
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564
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Merging of Human and Mouse SingleCellExperiment Objects Error
SingleCellExperiment
3 months ago Dario Strbenac ★ 1.5k
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rpk per cell saved in SCE object.
SingleCellExperiment
3 months ago JalapenoCornbread • 0
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2
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935
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Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
4 months ago elgomez • 0
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3
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495
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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
updated 4 months ago by • 0 • written 5 months ago by • 0
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505
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Subsetting cells from a single cell experiment
SingleCellExperiment
written 6 months ago by • 0
1
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5
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852
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Recommendation for large.n in filterByExpr
scRNAseq edgeR SingleCellExperiment
8 months ago duez.tolga • 0
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2
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901
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
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2
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824
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runPCA in a SingleCellExperiment results ina colMeans error
scran SingleCellExperiment
10 months ago Lluís Revilla Sancho ▴ 730
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3
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2.0k
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Remove certain highly expressing cells from a SCE
SingleCellExperiment
12 months ago mollyab12 • 0
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1
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1.0k
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Rename colData column
SingleCellExperiment colData rename
updated 14 months ago by ▴ 780 • written 14 months ago by ▴ 10
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3
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1.6k
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How to work with dplyr verbs in the colData slot of SingleCellExperiment objects?
SingleCellExperiment
updated 15 months ago by ▴ 10 • written 5.3 years ago by ▴ 10
2
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3
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1.6k
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Efficiently working with HDF5-backed SingleCellExperiments
HDF5Array SingleCellExperiment DelayedArray
20 months ago • updated 19 months ago merv ▴ 120
2
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2
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789
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
20 months ago • updated 19 months ago k1m ▴ 20
2
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4
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914
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
20 months ago • updated 19 months ago Romina • 0
1
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1
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1.1k
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Extract only dataframes from AnnData objects
rhdf5 HDF5Array anndata SingleCellExperiment
updated 20 months ago by ▴ 740 • written 20 months ago by ▴ 120
4
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1
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2.2k
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How to save `SingleCellExperiment` with `DelayedArray` assay(s) in a portable format?
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
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1.0k
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Combining multiple MTX (matrix market) files to HDF5 Array format
HDF5Array SingleCellExperiment DelayedArray
20 months ago merv ▴ 120
4
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3
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1.5k
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SingleCellExperiment: Edit cluster IDs in colLabels
scran Clustering SingleCellExperiment annotate cluster
updated 21 months ago by 65k • written 21 months ago by ▴ 10
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1
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972
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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 22 months ago by ★ 4.1k • written 22 months ago by • 0
2
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5
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4.1k
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Merging multiple single cell experiment objects from different samples
sce SingleCellExperiment merge
updated 14 months ago by • 0 • written 2.0 years ago by ▴ 10
2
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1
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1.1k
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Getting error Creating SingleCellExperiment instances "all assays must have the same nrow and ncol"
SingleCellExperiment scran scater
updated 2.1 years ago by ▴ 780 • written 2.1 years ago by • 0
1
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2
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925
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How to answer reviewers question of physical cell size influencing single cell results?
SingleCellExperiment scater ExperimentalDesign scran
2.2 years ago msn ▴ 10
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1
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718
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Affymetrix chip which is not listed on this webpage
SingleCellExperiment
updated 2.3 years ago by 65k • written 2.3 years ago by • 0
2
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2
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1.2k
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velociraptor preparation
SingleCellExperiment singlecell velociraptor scvelo
updated 2.4 years ago by ★ 4.1k • written 2.4 years ago by ▴ 40
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0
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635
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scRNA technical replicates in separate runs
SingleCellExperiment scRNAseq
2.4 years ago Núria • 0
1
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2
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842
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Splatter: which parameters can cause individual variability( expression levels of genes should change across samples)
SingleCellExperiment splatter
2.5 years ago Fatima • 0
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3
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1.7k
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Ensuring reproducibility in BiocParallel SingleCellExperiment workflows
scater SingleCellExperiment BiocParallel scuttle scran
2.5 years ago enricoferrero ▴ 660
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1
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2.6k
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Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by • 0
2
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5
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4.9k
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Error in conversion of SCE object to Seurat Object.
SingleCellExperiment
updated 2.9 years ago by ▴ 60 • written 3.0 years ago by ▴ 20
2
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3
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1.3k
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how to stop plotDots() from sorting my features (genes) ?
SingleCellExperiment scater
updated 3.2 years ago by ▴ 160 • written 3.2 years ago by • 0
3
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2
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2.2k
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Merging only those samples sequenced over multiple batches - scRNA-seq
SingleCell SingleCellExperiment scater
3.2 years ago camerond • 0
0
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7
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2.1k
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SingleCellExperiment package: storing reducedDims metadata
SingleCellExperiment
3.3 years ago • updated 3.2 years ago bge • 0
1
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3
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1.9k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 10
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5
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2.3k
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scuttle::aggregateAcrossCells() crashes R on large SingleCellExperiment
scran SingleCellExperiment scuttle scater
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 660
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2
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1.2k
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from phenograph output to singlecellexperiment object with metadata
SingleCellExperiment
3.4 years ago achaillon • 0
1
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3
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1.0k
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singlecellexperiments markers after clustering
CATALYST SingleCellExperiment
updated 3.4 years ago by ▴ 70 • written 3.4 years ago by • 0
1
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3
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1.5k
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SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.4 years ago achaillon • 0
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2
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1.4k
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Removal of cell cycle effect using batchelor::regressBatches() and proper usage of corrected UMI matrix
scRNAseq batchelor SingleCell SingleCellExperiment scran
3.4 years ago jirkanov • 0
1
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2
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2.0k
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Error when converting Seurat to SingleCellExperiment
Seurat SingleCellExperiment
3.4 years ago lirongrossmann ▴ 40
0
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1
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831
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improving running time of runNMF
runNMF scater singlecell SingleCellExperiment
updated 3.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
2
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7
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2.6k
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How to run runNMF in parallel?
scater single SingleCellExperiment
updated 2.5 years ago by ★ 28k • written 3.5 years ago by ▴ 40
0
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6
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2.6k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 80
1
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1
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1.2k
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Biological replicates in single cell experiments DE
singleCellExperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by • 0
0
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4
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1.3k
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marker genes in single cell experiment
single cell singlecellexperiment gene markers
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
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0
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747
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Single cell WGS and ATAC-seq tools
single cell singlecellexperiment atac seq WGS
3.7 years ago lirongrossmann ▴ 80
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3
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2.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
1
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2
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1.8k
views
ident function in sce
SingleCellExperiment cluster identities sce
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
0
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1
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1.2k
views
Clearer error messages in SingleCellExperiment cbind
singlecellexperiment sce scater
updated 4.0 years ago by ★ 28k • written 4.0 years ago by • 0
2
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4
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2.3k
views
Quality control in SingleCellExperiment
SingleCellExperiment scater sce quality control
updated 3.3 years ago by • 0 • written 4.1 years ago by • 0
50 results • Page 1 of 1
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Answer: Once again a "Model matrix not full rank" by swbarnes2 ★ 1.3k
Replicate numbers, like the 1 in control_1 are fine in sample names, but never add them to anything else in colData. From the computer's p…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
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Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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