Showing : singleR • reset
2
votes
2
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604
views
SingleR with multiple single cell references
SingleR scran
9 weeks ago • updated 17 days ago maltethodberg ▴ 180
0
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0
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143
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Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 weeks ago Muhammad • 0
0
votes
2
replies
49k
views
SingleR Label.Ont
SingleR
written 19 months ago by • 0
1
vote
1
reply
525
views
segfault when using singleR with Azimuth reference
SingleR
updated 6 months ago by 68k • written 6 months ago by ▴ 760
0
votes
2
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843
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 28 days ago by • 0 • written 9 months ago by ▴ 70
0
votes
1
reply
645
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 10 months ago by ★ 4.8k • written 10 months ago by • 0
0
votes
3
replies
1.3k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 15 months ago by • 0
1
vote
2
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1.5k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
16 months ago elgomez • 0
1
vote
4
replies
4.8k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 16 months ago by ▴ 50
2
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4
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3.6k
views
SingleR annotation of several slots/patients
SingleR
written 16 months ago by ▴ 50
0
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1
reply
613
views
SingleR Book Not Found
SingleR
updated 17 months ago by ▴ 750 • written 17 months ago by • 0
1
vote
2
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2.6k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 17 months ago by ★ 4.8k • written 17 months ago by ★ 1.5k
0
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2
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1.8k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
22 months ago Matvii Mykhailichenko • 0
0
votes
4
replies
4.7k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 22 months ago by • 0 • written 5.4 years ago by • 0
0
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0
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939
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
22 months ago Yijing • 0
1
vote
4
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2.0k
views
SingleR and gcc-8.3.0
gcc SingleR
updated 2.1 years ago by ▴ 20 • written 2.1 years ago by ▴ 10
0
votes
1
reply
1.3k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.1 years ago by ▴ 750 • written 2.1 years ago by ▴ 10
0
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1
reply
965
views
input for singR function
Seurat_object singe-cell singleR
updated 12 weeks ago by • 0 • written 2.2 years ago by • 0
0
votes
1
reply
1.2k
views
SingleR error with multiple references
SingleR
updated 23 months ago by • 0 • written 2.4 years ago by • 0
1
vote
1
reply
1.1k
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SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 2.5 years ago by ★ 4.8k • written 2.5 years ago by • 0
0
votes
1
reply
1.8k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.7 years ago by ★ 4.8k • written 2.7 years ago by • 0
0
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0
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1.5k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.8 years ago Guandong Shang ▴ 40
3
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4
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2.6k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
3.0 years ago rohitsatyam102 ▴ 20
0
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1
reply
1.5k
views
celldex error when downloading reference datasets
celldex SingleR
updated 3.2 years ago by ★ 28k • written 3.2 years ago by • 0
15
votes
13
replies
4.1k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 3.5 years ago by ▴ 10 • written 3.5 years ago by ▴ 20
0
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1
reply
3.5k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.7 years ago by ★ 4.8k • written 3.7 years ago by • 0
0
votes
2
replies
4.8k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 3.1 years ago by • 0 • written 3.8 years ago by • 0
2
votes
3
replies
5.2k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
3.8 years ago • updated 3.7 years ago Imtiaz ▴ 10
2
votes
2
replies
3.6k
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 17 months ago by ★ 1.5k • written 4.0 years ago by ▴ 10
1
vote
1
reply
2.1k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR ImmgenData() mouseRNAseqData()
updated 4.2 years ago by ★ 6.6k • written 4.2 years ago by • 0
0
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1
reply
3.0k
views
SingleR and SCTransform
SingleR
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 20
2
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3
replies
2.1k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
4.4 years ago • updated 4.3 years ago achaillon • 0
1
vote
5
replies
1.8k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 4.5 years ago by • 0 • written 4.5 years ago by ▴ 10
1
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1
reply
1.9k
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 4.6 years ago by ★ 28k • written 4.6 years ago by • 0
0
votes
6
replies
3.5k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 80
1
vote
3
replies
1.8k
views
Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 80
0
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2
replies
1.9k
views
most correlated genes in SingleR
singlecell singleR
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 50
0
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1
reply
2.1k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 50
0
votes
3
replies
2.7k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 4.7 years ago by ★ 28k • written 4.7 years ago by ▴ 50
8
votes
16
replies
8.8k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 4.7 years ago by 4.1k • written 4.7 years ago by ▴ 680
0
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1
reply
1.6k
views
pheatmap needs to be manually added to plot heatmaps
singler bug
5.1 years ago muad.abdelhay ▴ 10
0
votes
1
reply
1.6k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR MouseGastrulationData
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 70
2
votes
4
replies
1.8k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 5.2 years ago by ★ 28k • written 5.3 years ago by ▴ 120
1
vote
2
replies
2.1k
views
Error with cell annotation using singleR
SingleR
updated 5.3 years ago by ★ 13k • written 5.3 years ago by ▴ 10
44 results • Page 1 of 1
Recent ...
Replies
Comment: CluserProfiler message "No gene can be mapped" by Carolina • 0
There is, the overlap that reads out is ( Genes in common: 368 of 368 ). Here is the link for [background genes][1], [term2gene][2], [term2…
Comment: Differing results with DESeq2 by JKim • 0
My two cents. I think it would be more straightforward if you use cellmeans model. Have a look at [A guide to creating design matrices for …
Answer: CluserProfiler message "No gene can be mapped" by James W. MacDonald 68k
Your gene IDs are things like this: `Mpyr-NLJ1B.v3.hap1.scaffold1.g290550`, and the genes in your term2gene table are things like this: `Mp…
Answer: RNA-seq input to GRaNIE by James W. MacDonald 68k
This is [covered in the vignette.][1] [1]: https://bioconductor.org/packages/release/bioc/vignettes/GRaNIE/inst/doc/GRaNIE_packageDe…
Answer: Help using reduceSimMatrix with a custom annotation by sergisayolspuig ▴ 80
Hi there, `reduceSimMatrix()` expects a "GOALL" keytype in the OrgDb object when called with `children=TRUE` (which is the default for thi…
Votes
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
A: Unbalanced experiment with multiple samples from each patient.
A: Understanding contrasts limma
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