Showing : SingleCellData • reset
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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 5 days ago by 68k • written 5 days ago by • 0
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64
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
15 days ago Muhammad • 0
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2
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690
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
4 months ago José • 0
0
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1
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490
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 6 months ago by 68k • written 6 months ago by • 0
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1
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522
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Dimensionality reduction visualization
imcRtools SingleCellData imcdatasets SpatialWorkflow
updated 13 months ago by 68k • written 13 months ago by • 0
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2.2k
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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 15 months ago by • 0
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2
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723
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 15 months ago by ★ 4.7k • written 15 months ago by • 0
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3
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1.1k
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insufficient unique points for computing knee/inflection points
DropletUtils SingleCellData
updated 19 months ago by ★ 4.7k • written 19 months ago by • 0
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2
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1.7k
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
20 months ago Matvii Mykhailichenko • 0
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975
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Job: Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData ComputationalBiology
23 months ago Chrysothemis ▴ 10
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1.0k
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Job: Job as a bioinformatician in Hamburg, Germany
DimensionReduction SingleCellData multiomics MachineLearning
2.2 years ago Diego's • 0
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734
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Gene Id duplicated
SingleCell SingleCellData
updated 2.4 years ago by ★ 4.7k • written 2.4 years ago by • 0
2
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2
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1.1k
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.5 years ago k1m ▴ 20
2
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4
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1.3k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.5 years ago Romina • 0
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1
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1.2k
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Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData splatter
updated 2.8 years ago by ▴ 50 • written 2.8 years ago by • 0
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1
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1.0k
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Running PLAGE gets killed
GSVA SingleCellData
updated 3.0 years ago by ★ 3.4k • written 3.0 years ago by • 0
2
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1
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2.2k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.1 years ago by 68k • written 3.1 years ago by • 0
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3
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2.3k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.1 years ago by ★ 28k • written 4.2 years ago by ▴ 10
18 results • Page 1 of 1
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Replies
Comment: how many significant figures are there in DESeq2 output by ATpoint ★ 4.7k
If you want consistency then use a fixed software environment like Docker, wirh fixed code and thresholds that make sense. Rounding to near…
Comment: Compare TCGA-PAAD with GTEx gene expression by Jane • 0
why aren't there any answers?
Comment: Too many significant genes when integrating gtex and tcga by Jane • 0
I encountered the same issue: too many DEGs after limma analysis. It is sad that until today we can still see the paper published where GTE…
Comment: how many significant figures are there in DESeq2 output by Matthew McCormack ▴ 180
Thank you for your reply. It is good to know that cutoff of 0.05 means less than 0.05. My concerns are about consistency and reproducibili…
Comment: DiffBind edgeR normalization --- why are the normalization factors all equal to by ATpoint ★ 4.7k
No, normalization factors from edgeR rather than size factors from DESeq2 are not proportional, it's a different concept and implementation…
Votes
A: Unbalanced experiment with multiple samples from each patient.
Unbalanced experiment with multiple samples from each patient.
Answer: Vertical line at A=0, nothing else, on MA plot
Answer: GSVA Error Code "Calling gsva(expr=., gset.idx.list=., method=., ...) is defunct
Answer: Group-specific condition effects with individuals nested: matrix is not full ra
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