Showing : SingleCellData • reset
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
11 weeks ago Ludwig Geistlinger ▴ 70
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
5 months ago Konstantinos Yeles ▴ 90
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How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData DESeq2 pseudobulk sing
updated 8 months ago by 68k • written 8 months ago by • 0
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 months ago Muhammad • 0
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1.1k
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
13 months ago • updated 12 months ago José • 0
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689
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 15 months ago by 68k • written 15 months ago by • 0
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Dimensionality reduction visualization
imcRtools SingleCellData imcdatasets SpatialWorkflow
updated 22 months ago by 68k • written 22 months ago by • 0
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3.8k
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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 23 months ago by • 0
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2
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974
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 24 months ago by ★ 5.0k • written 24 months ago by • 0
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insufficient unique points for computing knee/inflection points
DropletUtils SingleCellData
updated 2.3 years ago by ★ 5.0k • written 2.3 years ago by • 0
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.4 years ago Matvii Mykhailichenko • 0
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Job: Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData ComputationalBiology
2.6 years ago Chrysothemis ▴ 10
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Job: Job as a bioinformatician in Hamburg, Germany
DimensionReduction SingleCellData multiomics MachineLearning
2.9 years ago Diego's • 0
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946
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Gene Id duplicated
SingleCell SingleCellData
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 3 months ago by • 0 • written 3.2 years ago by ▴ 20
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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
3.2 years ago Romina • 0
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1
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1.4k
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Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData splatter
updated 3.5 years ago by ▴ 50 • written 3.6 years ago by • 0
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1.2k
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Running PLAGE gets killed
GSVA SingleCellData
updated 3.7 years ago by ★ 3.4k • written 3.7 years ago by • 0
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1
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2.5k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.8 years ago by 68k • written 3.8 years ago by • 0
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3
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2.5k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.8 years ago by ★ 29k • written 4.9 years ago by ▴ 10
20 results • Page 1 of 1
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Comment: Getting a large intercept with DESeq2 by Michael Love 43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2 by James W. MacDonald 68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2 by James W. MacDonald 68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C by ATpoint ★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa? by Gordon Smyth 53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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