Showing : singler • reset
0
votes
3
replies
53k
views
SingleR Label.Ont
SingleR
written 2.2 years ago by • 0
2
votes
2
replies
1.0k
views
SingleR with multiple single cell references
SingleR scran
9 months ago • updated 8 months ago maltethodberg ▴ 180
0
votes
0
replies
406
views
Help with mouse cell type annotation
annotation SingleR mouse SingleCellData scRNAseq
9 months ago Muhammad • 0
1
vote
1
reply
764
views
segfault when using singleR with Azimuth reference
SingleR
updated 14 months ago by 68k • written 14 months ago by ▴ 760
0
votes
2
replies
1.1k
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 8 months ago by • 0 • written 16 months ago by ▴ 70
0
votes
1
reply
808
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 18 months ago by ★ 5.0k • written 18 months ago by • 0
0
votes
3
replies
1.5k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 23 months ago by • 0
1
vote
2
replies
1.8k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
24 months ago elgomez • 0
1
vote
4
replies
6.3k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 24 months ago by ▴ 50
2
votes
4
replies
4.2k
views
SingleR annotation of several slots/patients
SingleR
written 2.0 years ago by ▴ 50
0
votes
1
reply
808
views
SingleR Book Not Found
SingleR
updated 2.0 years ago by ▴ 760 • written 2.0 years ago by • 0
1
vote
2
replies
3.1k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 2.1 years ago by ★ 5.0k • written 2.1 years ago by ★ 1.5k
0
votes
2
replies
2.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
2.4 years ago Matvii Mykhailichenko • 0
0
votes
4
replies
5.1k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 2.5 years ago by • 0 • written 6.0 years ago by • 0
0
votes
0
replies
1.1k
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
2.5 years ago Yijing • 0
1
vote
4
replies
2.4k
views
SingleR and gcc-8.3.0
gcc SingleR
updated 2.7 years ago by ▴ 20 • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.6k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by ▴ 10
0
votes
1
reply
1.1k
views
input for singR function
Seurat_object singe-cell singleR
updated 10 months ago by • 0 • written 2.8 years ago by • 0
0
votes
1
reply
1.4k
views
SingleR error with multiple references
SingleR
updated 2.5 years ago by • 0 • written 3.0 years ago by • 0
1
vote
1
reply
1.2k
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 3.1 years ago by ★ 5.0k • written 3.1 years ago by • 0
0
votes
1
reply
1.9k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 3.3 years ago by ★ 5.0k • written 3.3 years ago by • 0
0
votes
0
replies
1.7k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
3.4 years ago Guandong Shang ▴ 40
3
votes
4
replies
2.9k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
3.7 years ago • updated 3.6 years ago rohitsatyam102 ▴ 20
0
votes
1
reply
1.8k
views
celldex error when downloading reference datasets
celldex SingleR
updated 3.8 years ago by ★ 29k • written 3.8 years ago by • 0
15
votes
13
replies
4.7k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 4.1 years ago by ▴ 10 • written 4.1 years ago by ▴ 20
0
votes
1
reply
3.8k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 4.3 years ago by ★ 5.0k • written 4.3 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 3.7 years ago by • 0 • written 4.4 years ago by • 0
2
votes
3
replies
5.6k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
4.5 years ago • updated 4.3 years ago Imtiaz ▴ 10
2
votes
2
replies
4.0k
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 2.1 years ago by ★ 1.5k • written 4.6 years ago by ▴ 10
1
vote
1
reply
2.2k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR ImmgenData() mouseRNAseqData()
updated 4.8 years ago by ★ 6.6k • written 4.8 years ago by • 0
0
votes
1
reply
3.3k
views
SingleR and SCTransform
SingleR
updated 4.8 years ago by ★ 29k • written 4.8 years ago by ▴ 20
2
votes
3
replies
2.4k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
5.0 years ago achaillon • 0
1
vote
5
replies
2.1k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 5.1 years ago by • 0 • written 5.1 years ago by ▴ 10
1
vote
1
reply
2.1k
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 5.2 years ago by ★ 29k • written 5.2 years ago by • 0
0
votes
6
replies
3.8k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 80
1
vote
3
replies
2.1k
views
Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 80
0
votes
2
replies
2.1k
views
most correlated genes in SingleR
singlecell singleR
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
0
votes
1
reply
2.4k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
0
votes
3
replies
2.9k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 5.3 years ago by ★ 29k • written 5.3 years ago by ▴ 50
8
votes
16
replies
9.5k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 5.3 years ago by 4.2k • written 5.3 years ago by ▴ 680
0
votes
1
reply
1.7k
views
pheatmap needs to be manually added to plot heatmaps
singler bug
5.7 years ago muad.abdelhay ▴ 10
0
votes
1
reply
1.9k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR MouseGastrulationData
updated 5.7 years ago by ★ 29k • written 5.7 years ago by ▴ 70
2
votes
4
replies
2.0k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 5.9 years ago by ★ 29k • written 5.9 years ago by ▴ 120
1
vote
2
replies
2.3k
views
Error with cell annotation using singleR
SingleR
updated 5.9 years ago by ★ 13k • written 5.9 years ago by ▴ 10
44 results • Page 1 of 1
Recent ...
Replies
Answer: PTM analysis in LIMPA by Gordon Smyth 53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR by James W. MacDonald 68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k
It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …
Comment: problem reading bam files into nucleR by efoss ▴ 10
I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…
Answer: two questions about limma by Gordon Smyth 53k
Answered here: https://support.bioconductor.org/p/16318/
Votes
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
Comment: upstream git branches of bioc-release
Awards • All
Commentator to sina.nassiri ▴ 130
Popular Question to Hervé Pagès 16k
Popular Question to jared.andrews07 ▴ 30
Popular Question to James W. MacDonald 68k
Popular Question to shepherl 4.2k
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