Showing : SingleCellData • reset
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News: Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment SingleCell SingleCellWorkflow SingleCellData
5 months ago Ludwig Geistlinger ▴ 80
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Possible issue following the logNormCounts(filtered) with resulted fit
single-cell SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
8 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 11 months ago by 68k • written 11 months ago by • 0
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
12 months ago Muhammad • 0
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
16 months ago • updated 15 months ago José • 0
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 18 months ago by 68k • written 18 months ago by • 0
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Dimensionality reduction visualization
imcRtools SingleCellData imcdatasets SpatialWorkflow
updated 2.1 years ago by 68k • written 2.1 years 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 2.2 years ago by • 0
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by • 0
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insufficient unique points for computing knee/inflection points
DropletUtils SingleCellData
updated 2.5 years ago by ★ 5.0k • written 2.5 years ago by • 0
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.6 years ago Matvii Mykhailichenko • 0
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Job: Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData ComputationalBiology
2.9 years ago Chrysothemis ▴ 10
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Job: Job as a bioinformatician in Hamburg, Germany
DimensionReduction SingleCellData multiomics MachineLearning
3.2 years ago Diego's • 0
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Gene Id duplicated
SingleCell SingleCellData
updated 3.4 years ago by ★ 5.0k • written 3.4 years ago by • 0
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
updated 6 months ago by • 0 • written 3.4 years ago by ▴ 20
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4
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1.8k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
3.4 years ago Romina • 0
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1.5k
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Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData splatter
updated 3.8 years ago by ▴ 50 • written 3.8 years ago by • 0
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1.3k
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Running PLAGE gets killed
GSVA SingleCellData
updated 3.9 years ago by ★ 3.4k • written 3.9 years ago by • 0
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1
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2.9k
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 4.1 years ago by 68k • written 4.1 years ago by • 0
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 5.1 years ago by ★ 29k • written 5.1 years ago by ▴ 10
20 results • Page 1 of 1
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Comment: Which preprocessing steps are needed before running limpa? by miro165sabo • 0
Hi @gordonsmyth, thank you a lot for very fast and valuable response. I edited the question to provide more details.
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ? by Gordon Smyth 53k
I tend to use dpcCN(), because it more robust than dpc() to experiments with lots of samples and big differences between samples. You coul…
Answer: Which preprocessing steps are needed before running limpa? by Gordon Smyth 53k
Please see the example limpa analyses given at <http://github.com/smythlab/limpa>, especially the kidney cancer case study. limpa does not…
Comment: Why does IDTaxa trainingSet for SILVA contain "_2" suffixes in the taxonomy name by Korneel • 0
Thanks for the quick reply! If I understand correctly, I think if I keep track of the full lineage, I shouldn't have any risk of collapsin…
Comment: Pathway abundance data from Curatedmetagenomics by yesquokkan • 0
Hello, I was also wondering about the same issue. Did you figure it out?
Votes
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Which preprocessing steps are needed before running limpa?
Answer: Should I use beta1 from limpa::dpc() or limpa::dpcCN(), if they differ?
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