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Seurat
•
reset
0
votes
3
replies
338
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
updated 15 days ago by
jodan
• 0 • written 23 days ago by
Quang NN
▴ 10
0
votes
2
replies
750
views
How to add Ensembl ids after Pseudobulk analysis by DESeq2
Seurat
DESeq2
single-cell
scRNA
Pseudobulk
updated 8 months ago by
Guido Hooiveld
★ 4.1k • written 8 months ago by
Sara
• 0
0
votes
5
replies
1.7k
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk
seurat
DESeq2
updated 14 months ago by
Kevin Blighe
★ 4.0k • written 14 months ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
2.0k
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 15 months ago by
ATpoint
★ 4.7k • written 15 months ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
4.5k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 20 months ago by
Marco
• 0 • written 5.2 years ago by
mathai.c
• 0
3
votes
1
reply
1.1k
views
'Seurat' package
singlecell
seurat
updated 21 months ago by
ATpoint
★ 4.7k • written 21 months ago by
Sooni
▴ 10
0
votes
2
replies
1.3k
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore
DotPlot
hdWGNCA
Seurat
22 months ago
Yuko
• 0
0
votes
1
reply
4.0k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 2.0 years ago by
ATpoint
★ 4.7k • written 2.0 years ago by
bio.boi
• 0
1
vote
2
replies
1.2k
views
Error with FindConservedMarkers()
seurat
2.0 years ago
Chris
▴ 20
1
vote
0
replies
2.1k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
2.0 years ago
cathalgking
▴ 10
2
votes
1
reply
2.1k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 3.1 years ago by
James W. MacDonald
68k • written 3.1 years ago by
NGS_enthusiast
• 0
0
votes
3
replies
1.9k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
3.2 years ago
zahra.mesri95
• 0
1
vote
1
reply
1.5k
views
Seurat: normalized data in the integrated assay
seurat
updated 3.7 years ago by
Peter Hickey
▴ 750 • written 3.7 years ago by
zli1
• 0
5
votes
15
replies
15k
views
Can't able to install Seurat in Rstudio
Rstudio
Seurat
updated 3.7 years ago by
Kevin Blighe
★ 4.0k • written 3.7 years ago by
KOUSTAV
• 0
0
votes
0
replies
838
views
Using csClassify on a SeuratObject
scRNAseq
csClassify
Seurat
updated 3.7 years ago by
ATpoint
★ 4.7k • written 3.8 years ago by
curiousmind007
▴ 10
2
votes
2
replies
2.6k
views
Error when converting Seurat to SingleCellExperiment
Seurat
SingleCellExperiment
4.2 years ago
lirongrossmann
▴ 50
6
votes
3
replies
3.7k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport
Seurat
Smart-Seq
Smart-Seq2
updated 4.6 years ago by
Michael Love
43k • written 4.6 years ago by
lshepard
▴ 40
3
votes
6
replies
3.6k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
heir_of_isildur88
• 0
5
votes
1
reply
2.0k
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
tobias-messmer
▴ 20
0
votes
2
replies
2.0k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
5.3 years ago
albadrs.93
▴ 10
0
votes
3
replies
2.2k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 5.3 years ago by
Martin Morgan
25k • written 5.3 years ago by
moldach
▴ 20
2
votes
2
replies
3.1k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq
Seurat
DE
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
ilee8
• 0
2
votes
4
replies
4.2k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 12 months ago by
Gordon Smyth
52k • written 5.6 years ago by
sambunga094
• 0
1
vote
3
replies
13k
views
Seurat 2.3.4 installation
seurat
updated 5.8 years ago by
Gordon Smyth
52k • written 5.8 years ago by
Mike
▴ 10
1
vote
1
reply
1.5k
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq
seurat
CCA
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Bogdan
▴ 670
0
votes
1
reply
3.0k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 6.2 years ago by
Gordon Smyth
52k • written 6.2 years ago by
hamza_karakurt
▴ 60
0
votes
4
replies
3.3k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq
SEURAT
updated 6.2 years ago by
Steve Lianoglou
★ 13k • written 6.2 years ago by
Bogdan
▴ 670
1
vote
5
replies
2.9k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment
single-cell
rnaseq
seurat
scater
6.4 years ago
hamza_karakurt
▴ 60
1
vote
2
replies
13k
views
Seurat/DESeq2 - single cell RNA-seq differential expression
seurat
deseq2
updated 6.5 years ago by
Michael Love
43k • written 6.5 years ago by
Clara
▴ 10
0
votes
1
reply
5.3k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
6.8 years ago
Wolfgang Huber
★ 13k
6
votes
2
replies
6.0k
views
Cell type specific cell markers for Seurat based analysis.
single cell
seurat
clustering
updated 7.6 years ago by
ankur.chakravarthy.10
▴ 40 • written 7.6 years ago by
hrishi27n
▴ 20
31 results • Page
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Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
Comment: For some reason I can't update BiocManager to 3.20
by
azm.ana2
• 0
Sorry i apologize for the delay. Thank you very much for the answer. I have two supervisers and the one who knows about the computer is com…
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Answer: SingleR with multiple single cell references
by
Aaron Lun
★ 28k
> Is it necessary to piece together the individual steps manually (e.g. aggregateReference, trainSingleR, classifySingleR, combineRecompute…
Answer: Automatically install dependencies
by
ATpoint
★ 4.7k
The BiocManager, which is sort of an extended wrapper around `install.packages`, installs all R dependencies. If you see errors then this i…
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Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
A: Volcanoplot with limma - RAW P-values or Adj.P-Values
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