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Showing :
seurat
•
reset
3
votes
1
reply
121
views
'Seurat' package
singlecell
seurat
updated 24 days ago by
ATpoint
★ 2.9k • written 24 days ago by
Sooni
▴ 10
0
votes
2
replies
191
views
ModuleExprScore function/ hdWGNCA
ModuleExprScore
DotPlot
hdWGNCA
Seurat
8 weeks ago • updated 7 weeks ago
Yuko
• 0
0
votes
1
reply
548
views
DESeq2 after Seurat analysis on integrated datasets
DESeq2
SingleCell
GeneExpression
Seurat
updated 3 months ago by
ATpoint
★ 2.9k • written 3 months ago by
bio.boi
• 0
1
vote
2
replies
293
views
Error with FindConservedMarkers()
seurat
3 months ago
Chris
• 0
1
vote
0
replies
370
views
Convert SpatialExperiment Object to Seurat Object
scuttle
scater
seurat
SpatialExperiment
4 months ago
cathalgking
▴ 10
2
votes
1
reply
1.0k
views
Convert AnnotatedDataFrame S4 object from GEO datasets to Seurat Object
biobase
SingleCellData
seurat
SingleCell
updated 16 months ago by
James W. MacDonald
63k • written 16 months ago by
NGS_enthusiast
• 0
0
votes
3
replies
910
views
NA values for mitochondrial gene percentage
Seurat
scRNAseq
18 months ago
zahra.mesri95
• 0
1
vote
1
reply
870
views
Seurat: normalized data in the integrated assay
seurat
updated 24 months ago by
Peter Hickey
▴ 650 • written 24 months ago by
zli1
• 0
5
votes
15
replies
6.7k
views
Can't able to install Seurat in Rstudio
Rstudio
Seurat
updated 2.0 years ago by
Kevin Blighe
3.8k • written 2.0 years ago by
KOUSTAV
• 0
0
votes
0
replies
414
views
Using csClassify on a SeuratObject
scRNAseq
csClassify
Seurat
updated 2.0 years ago by
ATpoint
★ 2.9k • written 2.0 years ago by
curiousmind007
▴ 10
1
vote
2
replies
1.2k
views
Error when converting Seurat to SingleCellExperiment
Seurat
SingleCellExperiment
2.5 years ago
lirongrossmann
▴ 40
5
votes
3
replies
2.5k
views
Full length single-cell RNA-seq - tximport output for downstream analysis
tximport
Seurat
Smart-Seq
Smart-Seq2
updated 2.9 years ago by
Michael Love
40k • written 2.9 years ago by
lshepard
▴ 40
3
votes
6
replies
2.1k
views
Carry over variable features when converting FastMNN SCE object to Seurat object
mnn
batchelor
scrna-seq
seurat
updated 3.0 years ago by
Aaron Lun
★ 28k • written 3.0 years ago by
heir_of_isildur88
• 0
4
votes
1
reply
965
views
Best practice for correlating scRNA seq to bulkRNA seq data
seurat
edgeR
spearman
correlation
scRNAseq
updated 3.1 years ago by
Aaron Lun
★ 28k • written 3.1 years ago by
tobias-messmer
▴ 10
0
votes
3
replies
2.3k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 3.5 years ago by
Gordon Smyth
47k • written 3.5 years ago by
mathai.c
• 0
0
votes
2
replies
1.1k
views
PCA outliers cleaning
scRNAseq
Pipeline
Seurat
SingleCellExperiment
3.6 years ago
albadrs.93
▴ 10
0
votes
3
replies
1.3k
views
Error: no applicable method for `RunTSNE` applied to an object of class "try-error"
Seurat
scRNA
debugging
exceptions
unit-test
updated 3.6 years ago by
Martin Morgan
25k • written 3.6 years ago by
moldach
▴ 20
2
votes
2
replies
2.2k
views
DE analysis for 10X scRNA-seq data with multiple conditions and multiple replicates
scRNA-seq
Seurat
DE
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
ilee8
• 0
2
votes
4
replies
3.3k
views
How to convert large gene counts data into matrix?
R
singlecell
bioinformatics
seurat
updated 2.3 years ago by
aedin
• 0 • written 3.9 years ago by
sambunga094
• 0
1
vote
3
replies
8.6k
views
Seurat 2.3.4 installation
seurat
updated 4.0 years ago by
Gordon Smyth
47k • written 4.1 years ago by
Mike
▴ 10
1
vote
1
reply
950
views
gene counts in Seurat after RunCCA() and AlignSubspace()
scRNA-seq
seurat
CCA
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 660
0
votes
1
reply
1.9k
views
Deconvolution Method in Seurat and convert from SingleCellExperiment
scater
seurat
singlecellexperiment
rnaseq
updated 4.5 years ago by
Gordon Smyth
47k • written 4.5 years ago by
hamza_karakurt
▴ 50
0
votes
4
replies
2.3k
views
scRNA-seq: a question about the names of the columns in a Seurat object
scRNA-seq
SEURAT
updated 4.5 years ago by
Steve Lianoglou
13k • written 4.5 years ago by
Bogdan
▴ 660
1
vote
5
replies
2.0k
views
newSCESet and SingleCellExperiment basic differences and TMM Normalization
singlecellexperiment
single-cell
rnaseq
seurat
scater
4.7 years ago • updated 4.6 years ago
hamza_karakurt
▴ 50
0
votes
2
replies
9.2k
views
Seurat/DESeq2 - single cell RNA-seq differential expression
seurat
deseq2
updated 4.8 years ago by
Michael Love
40k • written 4.8 years ago by
Clara
• 0
0
votes
1
reply
3.3k
views
Conversion to SingleCellExperiment from Seurat objects
Seurat
SingleCellExperiment
5.0 years ago
Wolfgang Huber
13k
6
votes
2
replies
4.6k
views
Cell type specific cell markers for Seurat based analysis.
single cell
seurat
clustering
updated 5.9 years ago by
ankur.chakravarthy.10
▴ 40 • written 5.9 years ago by
hrishi27n
▴ 20
27 results • Page
1 of 1
Recent ...
Replies
Answer: DESeq2 + analysis question for design with uneven time point design
by
Michael Love
40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge
by
Michael Love
40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Gordon Smyth
47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting
by
ATpoint
★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Anna
▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
Comment: Interpret plot from DiffBind
Answer: Use with_go along with other filters in getBM function
Answer: Use with_go along with other filters in getBM function
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Mike Smith
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Martin Morgan
25k
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deeenes
▴ 30
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Hervé Pagès
16k
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Gordon Smyth
47k
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