Showing : SingleCellData • reset
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
3 months ago Ludwig Geistlinger ▴ 70
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
6 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 9 months ago by 68k • written 9 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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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
13 months ago José • 0
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704
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 16 months ago by 68k • written 16 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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Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse R SingleCellExperiment SingleCellData
written 2.0 years ago by • 0
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2
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992
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 2.0 years ago by ★ 5.0k • written 2.1 years ago by • 0
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insufficient unique points for computing knee/inflection points
DropletUtils SingleCellData
updated 2.4 years ago by ★ 5.0k • written 2.4 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
2.7 years ago Chrysothemis ▴ 10
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Job: Job as a bioinformatician in Hamburg, Germany
DimensionReduction SingleCellData multiomics MachineLearning
3.0 years ago Diego's • 0
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Gene Id duplicated
SingleCell SingleCellData
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 4 months ago by • 0 • written 3.2 years ago by ▴ 20
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1.7k
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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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1.4k
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Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData splatter
updated 3.6 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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2.6k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.9 years ago by 68k • written 3.9 years ago by • 0
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3
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2.6k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 10
20 results • Page 1 of 1
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Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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