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SingleR
•
reset
15
votes
13
replies
3.0k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 2.5 years ago by
xiang
▴ 10 • written 2.5 years ago by
immuno.dh
▴ 20
8
votes
16
replies
6.2k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 3.8 years ago by
shepherl
3.9k • written 3.8 years ago by
enricoferrero
▴ 660
3
votes
4
replies
1.7k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
2.1 years ago • updated 24 months ago
rohitsatyam102
▴ 20
2
votes
2
replies
2.6k
views
After having the output from SingleR for cell type annotation, what's the next step to assign the cell type to each cluster
SingleCellSignalR
SingleCellWorkflow
SingleR
updated 5 months ago by
Assa Yeroslaviz
★ 1.5k • written 3.0 years ago by
FantasticAI
▴ 10
2
votes
4
replies
1.3k
views
Impose minimum restrictions on correlations in SingleR
single cell
R
SingleR
updated 4.3 years ago by
Aaron Lun
★ 28k • written 4.3 years ago by
k.vitting.seerup
▴ 120
2
votes
3
replies
3.7k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
2.9 years ago • updated 2.7 years ago
Imtiaz
▴ 10
2
votes
4
replies
1.3k
views
SingleR annotation of several slots/patients
SingleR
written 5 months ago by
Bine
▴ 40
1
vote
5
replies
1.5k
views
SingleR Error in getMethod(generic, "ANY")
singleR
rowMedians
getMethod
updated 3.5 years ago by
bongowongo
• 0 • written 3.5 years ago by
inzirio
▴ 10
1
vote
2
replies
1.6k
views
Error with cell annotation using singleR
SingleR
updated 4.3 years ago by
Steve Lianoglou
★ 13k • written 4.3 years ago by
bony.dekumar
▴ 10
1
vote
3
replies
1.3k
views
Raw counts for reference dataset in single cell rnaseq
single cell
celldex
singleR
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 80
1
vote
1
reply
1.3k
views
Does SingleR return output for every cell it's given or only those that it can provide an annotation for?
SingleR
Single Cell
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
w.gus.dunn
• 0
1
vote
3
replies
1.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset
SingleR
SingleCellExperiment
3.4 years ago
achaillon
• 0
1
vote
1
reply
1.5k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR
ImmgenData()
mouseRNAseqData()
updated 3.2 years ago by
Mike Smith
★ 6.5k • written 3.2 years ago by
Collins
• 0
1
vote
1
reply
724
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 18 months ago by
ATpoint
★ 4.1k • written 18 months ago by
mea2712
• 0
1
vote
2
replies
936
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR
SingleCellExperiment
4 months ago
elgomez
• 0
1
vote
2
replies
777
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 5 months ago by
ATpoint
★ 4.1k • written 5 months ago by
Assa Yeroslaviz
★ 1.5k
1
vote
4
replies
1.2k
views
SingleR and gcc-8.3.0
gcc
SingleR
updated 13 months ago by
Jovana Maksimovic
▴ 10 • written 14 months ago by
Fabien
▴ 10
1
vote
4
replies
1.7k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
written 4 months ago by
Bine
▴ 40
0
votes
1
reply
1.1k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 21 months ago by
ATpoint
★ 4.1k • written 21 months ago by
amit.korngut
• 0
0
votes
1
reply
2.6k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment
SummarizedExperiment
SingleR
updated 2.7 years ago by
ATpoint
★ 4.1k • written 2.7 years ago by
Gen
• 0
0
votes
1
reply
315
views
SingleR Book Not Found
SingleR
updated 5 months ago by
Peter Hickey
▴ 740 • written 5 months ago by
jgattiker
• 0
0
votes
1
reply
730
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 13 months ago by
Peter Hickey
▴ 740 • written 13 months ago by
cathalgking
▴ 10
0
votes
2
replies
3.7k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 2.1 years ago by
13304885395
• 0 • written 2.8 years ago by
ntourtillott23
• 0
0
votes
0
replies
530
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago
Yijing
• 0
0
votes
0
replies
476
views
input for singR function
Seurat_object
singe-cell
singleR
15 months ago
Paria
• 0
0
votes
3
replies
487
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 3 months ago by
Fayrouz
• 0
0
votes
0
replies
967
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
22 months ago
Guandong Shang
▴ 40
0
votes
4
replies
3.6k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 10 months ago by
Marco
• 0 • written 4.4 years ago by
mathai.c
• 0
0
votes
2
replies
904
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
10 months ago
Matvii Mykhailichenko
• 0
0
votes
3
replies
2.0k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
0
votes
2
replies
1.5k
views
most correlated genes in SingleR
singlecell
singleR
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
0
votes
4
replies
5.9k
views
SingleR Label.Ont
SingleR
updated 20 days ago by
lisia
• 0 • written 7 months ago by
saeed.khalili
• 0
0
votes
6
replies
2.6k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 80
0
votes
1
reply
1.2k
views
pheatmap needs to be manually added to plot heatmaps
singler
bug
4.1 years ago
muad.abdelhay
▴ 10
0
votes
1
reply
790
views
SingleR error with multiple references
SingleR
updated 11 months ago by
Irish
• 0 • written 17 months ago by
carlo
• 0
0
votes
1
reply
2.0k
views
SingleR and SCTransform
SingleR
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
amel.zulji
▴ 20
0
votes
1
reply
1.0k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR
MouseGastrulationData
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
jma1991
▴ 70
0
votes
1
reply
948
views
celldex error when downloading reference datasets
celldex
SingleR
updated 2.2 years ago by
Aaron Lun
★ 28k • written 2.2 years ago by
indigofreesia
• 0
0
votes
1
reply
1.4k
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
lirongrossmann
▴ 40
39 results • Page
1 of 1
Recent ...
Replies
Comment: fgsea significant result
by
Chris
• 0
Thanks ATpoint! Setting a fixed seed can reproduce the same result. However, if someone else analyze the same data with different seed, the…
Comment: SGSeq: moving toward diffex from SGSeq analysis
by
Sara
• 0
Thank you for your response. I have another question about saving the sgvc result as a CSV file. I would appreciate your help, please. ``` …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I tried different block lengths first and considered 100000 to be ideal because of the almost similar inter-range distance. S1= bootRange…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Michael Love
41k
The segmentation and block length are key parameters. We recommend for example blocks of length ~500kb. It would help if you would post yo…
Answer: Handling multiple differential expression comparisons
by
Michael Love
41k
It's typical that results are presented with each group having its own FDR control. So presenting each comparison with the adjusted p-va…
Votes
Handling multiple differential expression comparisons
Answer: fgsea significant result
Answer: fgsea significant result
package goseq seems to be not available on the latest version of R
package goseq seems to be not available on the latest version of R
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