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SingleCellData
•
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0
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134
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News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
11 weeks ago
Ludwig Geistlinger
▴ 70
1
vote
3
replies
1.2k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
5 months ago
Konstantinos Yeles
▴ 90
0
votes
1
reply
863
views
How to adjust for Cell Type Differences between groups in Pseudo-Bulk Differential Gene Expression analysis in scRNA-seq?
SingleCellData
DESeq2
pseudobulk
sing
updated 8 months ago by
James W. MacDonald
68k • written 8 months ago by
Sara
• 0
0
votes
0
replies
398
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
9 months ago
Muhammad
• 0
0
votes
2
replies
1.1k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
13 months ago • updated 12 months ago
José
• 0
0
votes
1
reply
689
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData
CEMiTool
updated 15 months ago by
James W. MacDonald
68k • written 15 months ago by
Menna
• 0
0
votes
1
reply
724
views
Dimensionality reduction visualization
imcRtools
SingleCellData
imcdatasets
SpatialWorkflow
updated 22 months ago by
James W. MacDonald
68k • written 22 months ago by
Simon
• 0
0
votes
10
replies
3.8k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
written 23 months ago by
Sitapriya
• 0
0
votes
2
replies
974
views
Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware
SingleCellData
annotationTools
updated 24 months ago by
ATpoint
★ 5.0k • written 24 months ago by
yw24418
• 0
0
votes
3
replies
1.4k
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 2.3 years ago by
ATpoint
★ 5.0k • written 2.3 years ago by
p.vlachou-efstathiou
• 0
0
votes
2
replies
2.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
2.4 years ago
Matvii Mykhailichenko
• 0
1
vote
0
replies
1.2k
views
Job:
Research Assistant - Computational Biology/Immunology, Memorial Sloan Kettering, New York
SingleCellData
ComputationalBiology
2.6 years ago
Chrysothemis
▴ 10
0
votes
0
replies
1.3k
views
Job:
Job as a bioinformatician in Hamburg, Germany
DimensionReduction
SingleCellData
multiomics
MachineLearning
2.9 years ago
Diego's
• 0
0
votes
0
replies
946
views
Gene Id duplicated
SingleCell
SingleCellData
updated 3.1 years ago by
ATpoint
★ 5.0k • written 3.1 years ago by
Romina
• 0
2
votes
4
replies
2.1k
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
updated 3 months ago by
Partly
• 0 • written 3.2 years ago by
k1m
▴ 20
2
votes
4
replies
1.6k
views
Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
3.2 years ago
Romina
• 0
0
votes
1
reply
1.4k
views
Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData
splatter
updated 3.5 years ago by
luke.zappia
▴ 50 • written 3.6 years ago by
Fatima
• 0
0
votes
1
reply
1.2k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 3.7 years ago by
Robert Castelo
★ 3.4k • written 3.7 years ago by
Amna
• 0
2
votes
1
reply
2.5k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.8 years ago by
James W. MacDonald
68k • written 3.8 years ago by
NGS_enthusiast
• 0
1
vote
3
replies
2.5k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 4.8 years ago by
Aaron Lun
★ 29k • written 4.9 years ago by
msn
▴ 10
20 results • Page
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Replies
Comment: Getting a large intercept with DESeq2
by
Michael Love
43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2
by
James W. MacDonald
68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2
by
James W. MacDonald
68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C
by
ATpoint
★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa?
by
Gordon Smyth
53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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