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
10 months ago Muhammad • 0
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
14 months ago • updated 13 months ago José • 0
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708
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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 23 months ago by 68k • written 23 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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998
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 2.1 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
2.5 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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967
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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 3.3 years ago by ▴ 20
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4
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1.7k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.3 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 3.6 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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Answer: NUPOP usage by shepherl 4.2k
You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…
Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0
In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …
Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
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…
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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