Showing : singleR • reset
0
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3
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54k
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SingleR Label.Ont
SingleR
written 2.3 years ago by • 0
2
votes
2
replies
1.2k
views
SingleR with multiple single cell references
SingleR scran
11 months ago • updated 9 months ago maltethodberg ▴ 180
0
votes
0
replies
432
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
11 months ago Muhammad • 0
1
vote
1
reply
838
views
segfault when using singleR with Azimuth reference
SingleR
updated 15 months ago by 68k • written 15 months ago by ▴ 760
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2
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1.1k
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 9 months ago by • 0 • written 17 months ago by ▴ 70
0
votes
1
reply
844
views
When I tried to use the functions from the celldex package to fetch information, I encountered the following error. How can I resolve this?"
celldex SingleR
updated 19 months ago by ★ 5.0k • written 19 months ago by • 0
0
votes
3
replies
1.6k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 2.0 years ago by • 0
1
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2
replies
1.9k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
2.1 years ago elgomez • 0
1
vote
4
replies
7.3k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 2.1 years ago by ▴ 50
2
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4
replies
4.7k
views
SingleR annotation of several slots/patients
SingleR
written 2.1 years ago by ▴ 50
0
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1
reply
842
views
SingleR Book Not Found
SingleR
updated 2.1 years ago by ▴ 760 • written 2.1 years ago by • 0
1
vote
2
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3.3k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 2.2 years ago by ★ 5.0k • written 2.2 years ago by ★ 1.5k
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
0
votes
4
replies
5.2k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 2.6 years ago by • 0 • written 6.1 years ago by • 0
0
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0
replies
1.1k
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
2.6 years ago Yijing • 0
1
vote
4
replies
2.5k
views
SingleR and gcc-8.3.0
gcc SingleR
updated 2.8 years ago by ▴ 20 • written 2.9 years ago by ▴ 10
0
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1
reply
1.6k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.8 years ago by ▴ 760 • written 2.8 years ago by ▴ 10
0
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1
reply
1.1k
views
input for singR function
Seurat_object singe-cell singleR
updated 11 months ago by • 0 • written 3.0 years ago by • 0
0
votes
1
reply
1.4k
views
SingleR error with multiple references
SingleR
updated 2.6 years ago by • 0 • written 3.2 years ago by • 0
1
vote
1
reply
1.3k
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 3.2 years ago by ★ 5.0k • written 3.2 years ago by • 0
0
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1
reply
2.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 3.5 years ago by ★ 5.0k • written 3.5 years ago by • 0
0
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0
replies
1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.5 years ago Guandong Shang ▴ 40
3
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4
replies
3.1k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
3.8 years ago • updated 3.7 years ago rohitsatyam102 ▴ 20
0
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1
reply
1.8k
views
celldex error when downloading reference datasets
celldex SingleR
updated 3.9 years ago by ★ 29k • written 3.9 years ago by • 0
15
votes
13
replies
4.8k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 4.2 years ago by ▴ 10 • written 4.2 years ago by ▴ 20
0
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1
reply
3.9k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.4 years ago by ★ 5.0k • written 4.4 years ago by • 0
0
votes
2
replies
5.1k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 3.8 years ago by • 0 • written 4.5 years ago by • 0
2
votes
3
replies
5.7k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
4.6 years ago • updated 4.4 years ago Imtiaz ▴ 10
2
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2
replies
4.1k
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 2.2 years ago by ★ 1.5k • written 4.7 years ago by ▴ 10
1
vote
1
reply
2.3k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR ImmgenData() mouseRNAseqData()
updated 4.9 years ago by ★ 6.6k • written 4.9 years ago by • 0
0
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1
reply
3.4k
views
SingleR and SCTransform
SingleR
updated 4.9 years ago by ★ 29k • written 4.9 years ago by ▴ 20
2
votes
3
replies
2.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
5.1 years ago achaillon • 0
1
vote
5
replies
2.1k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 5.2 years ago by • 0 • written 5.2 years ago by ▴ 10
1
vote
1
reply
2.2k
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 5.3 years ago by ★ 29k • written 5.3 years ago by • 0
0
votes
6
replies
4.0k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 80
1
vote
3
replies
2.2k
views
Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 80
0
votes
2
replies
2.2k
views
most correlated genes in SingleR
singlecell singleR
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
0
votes
1
reply
2.5k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
0
votes
3
replies
3.0k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 5.4 years ago by ★ 29k • written 5.4 years ago by ▴ 50
8
votes
16
replies
9.7k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 5.5 years ago by 4.3k • written 5.5 years ago by ▴ 680
0
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1
reply
1.8k
views
pheatmap needs to be manually added to plot heatmaps
singler bug
5.8 years ago muad.abdelhay ▴ 10
0
votes
1
reply
2.0k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR MouseGastrulationData
updated 5.8 years ago by ★ 29k • written 5.8 years ago by ▴ 70
2
votes
4
replies
2.0k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 6.0 years ago by ★ 29k • written 6.0 years ago by ▴ 120
1
vote
2
replies
2.4k
views
Error with cell annotation using singleR
SingleR
updated 6.0 years ago by ★ 13k • written 6.0 years ago by ▴ 10
44 results • Page 1 of 1
Recent ...
Replies
Answer: Quality control of shotgun metagenomics data by James W. MacDonald 68k
This support site is meant primarily for helping people with technical questions about using Bioconductor packages. For general analysis qu…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Votes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
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