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seurat
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0
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2
replies
186
views
How to compare expression levels of genes between scRNAseq and bulkRNAseq?
Seurat
RNASeq
DESeq2
scRNAseq
4 days ago • updated 1 day ago
Quang NN
▴ 10
0
votes
2
replies
705
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
1.6k
views
scRNA-seq as pseudobulk for DEseq2: does AggregateExpression() normalize counts?
pseudobulk
seurat
DESeq2
updated 13 months ago by
Kevin Blighe
★ 4.0k • written 13 months ago by
daiane.hemerichbrennan
• 0
1
vote
2
replies
1.9k
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 14 months ago by
ATpoint
★ 4.6k • written 14 months ago by
Assa Yeroslaviz
★ 1.5k
0
votes
4
replies
4.4k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 19 months ago by
Marco
• 0 • written 5.2 years ago by
mathai.c
• 0
3
votes
1
reply
1.0k
views
'Seurat' package
singlecell
seurat
updated 21 months ago by
ATpoint
★ 4.6k • written 21 months ago by
Sooni
▴ 10
0
votes
2
replies
1.2k
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore
DotPlot
hdWGNCA
Seurat
22 months ago • updated 21 months ago
Yuko
• 0
0
votes
1
reply
3.8k
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 23 months ago by
ATpoint
★ 4.6k • written 23 months ago by
bio.boi
• 0
1
vote
2
replies
1.2k
views
Error with FindConservedMarkers()
seurat
24 months ago
Chris
▴ 20
1
vote
0
replies
2.0k
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
24 months 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 3.0 years ago by
James W. MacDonald
67k • written 3.0 years ago by
NGS_enthusiast
• 0
0
votes
3
replies
1.9k
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
3.1 years ago
zahra.mesri95
• 0
1
vote
1
reply
1.5k
views
Seurat: normalized data in the integrated assay
seurat
updated 3.6 years ago by
Peter Hickey
▴ 750 • written 3.6 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
829
views
Using csClassify on a SeuratObject
scRNAseq
csClassify
Seurat
updated 3.7 years ago by
ATpoint
★ 4.6k • written 3.7 years ago by
curiousmind007
▴ 10
2
votes
2
replies
2.6k
views
Error when converting Seurat to SingleCellExperiment
Seurat
SingleCellExperiment
4.1 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 4.5 years ago by
Michael Love
43k • written 4.5 years ago by
lshepard
▴ 40
3
votes
6
replies
3.5k
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
1.9k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
5.2 years ago
albadrs.93
▴ 10
0
votes
3
replies
2.1k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 5.2 years ago by
Martin Morgan
25k • written 5.2 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
4.1k
views
How to convert large gene counts data into matrix?
R
Bioconductor
singlecell
bioinformatics
seurat
updated 11 months ago by
Gordon Smyth
52k • written 5.5 years ago by
sambunga094
• 0
1
vote
3
replies
13k
views
Seurat 2.3.4 installation
seurat
updated 5.7 years ago by
Gordon Smyth
52k • written 5.7 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 6.1 years ago by
Gordon Smyth
52k • written 6.1 years ago by
hamza_karakurt
▴ 60
0
votes
4
replies
3.2k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq
SEURAT
updated 6.1 years ago by
Steve Lianoglou
★ 13k • written 6.1 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
6.3 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
5.2k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
6.7 years ago
Wolfgang Huber
★ 13k
6
votes
2
replies
5.9k
views
Cell type specific cell markers for Seurat based analysis.
single cell
seurat
clustering
updated 7.5 years ago by
ankur.chakravarthy.10
▴ 40 • written 7.6 years ago by
hrishi27n
▴ 20
31 results • Page
1 of 1
Recent ...
Replies
Answer: I am having issues with bowtie2_build
by
James W. MacDonald
67k
Is proof.fa an actual FASTA file? Have you tried using the demo data that comes with the package? See the [vignette under Build Bowtie Inde…
Answer: DEG analysis across multiple timepoints, treatments and tissues
by
Michael Love
43k
Yes, if you think the entire time course can be modified by tissue effects then you would include another set of interaction terms. I re…
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!
Votes
Answer: Unable to install nloptr
Answer: ensembldb for Homo Sapiens organism containing superfluous SYMBOL genes?
C: How does edgeR cpm function calculate log(CPM) values?
Answer: Selection of correct coefficients or contrasts in DESeq2
Answer: Selection of correct coefficients or contrasts in DESeq2
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