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SingleCellData
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News:
Course: Single-cell analysis with R/Bioconductor
SingleCellExperiment
SingleCell
SingleCellWorkflow
SingleCellData
4 months ago
Ludwig Geistlinger
▴ 80
1
vote
3
replies
1.3k
views
Possible issue following the logNormCounts(filtered) with resulted fit
single-cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
7 months ago
Konstantinos Yeles
▴ 90
0
votes
1
reply
954
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 10 months ago by
James W. MacDonald
68k • written 10 months ago by
Sara
• 0
0
votes
0
replies
427
views
Help with mouse cell type annotation
annotation
SingleR
mouse
SingleCellData
scRNAseq
10 months ago
Muhammad
• 0
0
votes
2
replies
1.2k
views
Integration of Single Cell Experiments with batchelor::fastMNN
fastMNN
SingleCellData
BatchEffect
batchelor
14 months ago
José
• 0
0
votes
1
reply
724
views
Is CEMiTool for gene coexpression analysis suitable for single cell RNA Seq data?
SingleCellData
CEMiTool
updated 17 months ago by
James W. MacDonald
68k • written 17 months ago by
Menna
• 0
0
votes
1
reply
748
views
Dimensionality reduction visualization
imcRtools
SingleCellData
imcdatasets
SpatialWorkflow
updated 23 months ago by
James W. MacDonald
68k • written 23 months ago by
Simon
• 0
0
votes
10
replies
3.9k
views
Easiest way to convert read10xMolInfo data into a dataframe in R with gene labels as row names
tidyverse
R
SingleCellExperiment
SingleCellData
written 2.1 years ago by
Sitapriya
• 0
0
votes
2
replies
1.0k
views
Fail to annotate chromosome data to single cell sequencing data obtained from cellranger
AnnotationHubSoftware
SingleCellData
annotationTools
updated 2.1 years ago by
ATpoint
★ 5.0k • written 2.1 years ago by
yw24418
• 0
0
votes
3
replies
1.4k
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 2.4 years ago by
ATpoint
★ 5.0k • written 2.4 years ago by
p.vlachou-efstathiou
• 0
0
votes
2
replies
2.1k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
2.5 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
2.8 years ago
Chrysothemis
▴ 10
0
votes
0
replies
1.4k
views
Job:
Job as a bioinformatician in Hamburg, Germany
DimensionReduction
SingleCellData
multiomics
MachineLearning
3.1 years ago
Diego's
• 0
0
votes
0
replies
980
views
Gene Id duplicated
SingleCell
SingleCellData
updated 3.3 years ago by
ATpoint
★ 5.0k • written 3.3 years ago by
Romina
• 0
2
votes
4
replies
2.2k
views
How to detect LacZ tagged cells from single cell
SingleCell
SingleCellExperiment
SingleCellWorkflow
SingleCellData
updated 5 months ago by
Partly
• 0 • written 3.3 years ago by
k1m
▴ 20
2
votes
4
replies
1.7k
views
Summary of library size factor is all equal to one
SingleCell
SingleCellData
SingleCellWorkflow
SingleCellExperiment
3.3 years ago
Romina
• 0
0
votes
1
reply
1.5k
views
Splatter (unknown correlation between gene expression level in different cell types)
SingleCellData
splatter
updated 3.7 years ago by
luke.zappia
▴ 50 • written 3.7 years ago by
Fatima
• 0
0
votes
1
reply
1.3k
views
Running PLAGE gets killed
GSVA
SingleCellData
updated 3.8 years ago by
Robert Castelo
★ 3.4k • written 3.8 years ago by
Amna
• 0
2
votes
1
reply
2.6k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 4.0 years ago by
James W. MacDonald
68k • written 4.0 years ago by
NGS_enthusiast
• 0
1
vote
3
replies
2.6k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 5.0 years ago by
Aaron Lun
★ 29k • written 5.0 years ago by
msn
▴ 10
20 results • Page
1 of 1
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Replies
Comment: Guitar R package requires update due to dependency GenomicFeatures
by
ferran.llobet.cabau
▴ 10
Thank you @seandavi for your feedback. I followed your recommendations and generated a [pull request][1] including the fix for this issue…
Comment: Ensembl plants at annotationHub?
by
Guido Hooiveld
★ 4.1k
Hope you don't mind I am not Johannes... ;-) Note that you nowadays can generate these yourselves using the `docker` image Johannes made av…
Comment: How does contrasts.fit do in limma to extract comparisons with a model having in
by
jtsy6383
• 0
Thanks for the reminder about DiffVar (for that project I ended up using GAMLSS in the end and haven't touched DiffVar since) and the alter…
Comment: Ensembl plants at annotationHub?
by
jwp48
• 0
Dear Johannes, Would it be possible to generate a EnsDb for the newest Medicago V5 genome release? Medicago truncatula A17 r5.0 This woul…
Answer: please provide a BibTeX citation for "Advanced Single-Cell Analysis with Biocond
by
Ludwig Geistlinger
▴ 80
When referring to the OSCA book including individual sub-books please cite the OSCA paper: Amezquita, R.A., Lun, A.T.L., Becht, E. et a…
Votes
limma moderated t-statistics and B-statistics
Comment: Guitar R package requires update due to dependency GenomicFeatures
A: how to control age and gender effect in expression data using DESeq2
A: how to control age and gender effect in expression data using DESeq2
how to control age and gender effect in expression data using DESeq2
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