Showing : SingleCellData • reset
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Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN SingleCellData BatchEffect batchelor
3 months ago José • 0
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1
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462
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Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData CEMiTool
updated 5 months ago by 67k • written 5 months ago by • 0
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Dimensionality reduction visualization
imcRtools SingleCellData imcdatasets SpatialWorkflow
updated 12 months ago by 67k • written 12 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 14 months ago by • 0
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Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware SingleCellData annotationTools
updated 14 months ago by ★ 4.6k • written 14 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 18 months ago by ★ 4.6k • written 18 months ago by • 0
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Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
19 months ago Matvii Mykhailichenko • 0
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Job: Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData ComputationalBiology
22 months ago Chrysothemis ▴ 10
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Job: Job as a bioinformatician in Hamburg, Germany
DimensionReduction SingleCellData multiomics MachineLearning
2.1 years ago Diego's • 0
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717
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Gene Id duplicated
SingleCell SingleCellData
updated 2.3 years ago by ★ 4.6k • written 2.3 years ago by • 0
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How to detect LacZ tagged cells from single cell
SingleCell SingleCellExperiment SingleCellWorkflow SingleCellData
2.4 years ago k1m ▴ 20
2
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4
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1.2k
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Summary of library size factor is all equal to one
SingleCell SingleCellData SingleCellWorkflow SingleCellExperiment
2.4 years ago Romina • 0
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 2.7 years ago by ▴ 50 • written 2.8 years ago by • 0
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1.0k
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Running PLAGE gets killed
GSVA SingleCellData
updated 2.9 years ago by ★ 3.4k • written 2.9 years ago by • 0
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1
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Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase SingleCellData seurat SingleCell
updated 3.0 years ago by 67k • written 3.0 years ago by • 0
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3
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2.2k
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10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 4.1 years ago by ★ 28k • written 4.1 years ago by ▴ 10
16 results • Page 1 of 1
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Replies
Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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