Showing : singleR • reset
1
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206
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segfault when using singleR with Azimuth reference
SingleR
updated 4 weeks ago by 67k • written 5 weeks ago by ▴ 760
0
votes
3
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41k
views
SingleR Label.Ont
SingleR
written 13 months ago by • 0
0
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1
reply
526
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 3 months ago by ★ 4.5k • written 3 months ago by ▴ 70
0
votes
1
reply
503
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 4 months ago by ★ 4.5k • written 5 months ago by • 0
0
votes
3
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1.0k
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 10 months ago by • 0
1
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2
replies
1.2k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
10 months ago elgomez • 0
1
vote
4
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3.3k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 11 months ago by ▴ 50
2
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4
replies
2.5k
views
SingleR annotation of several slots/patients
SingleR
written 11 months ago by ▴ 50
0
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1
reply
496
views
SingleR Book Not Found
SingleR
updated 11 months ago by ▴ 740 • written 11 months ago by • 0
1
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2
replies
1.5k
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 11 months ago by ★ 4.5k • written 11 months ago by ★ 1.5k
0
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2
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1.4k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
16 months ago Matvii Mykhailichenko • 0
0
votes
4
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4.2k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat singleR
updated 16 months ago by • 0 • written 5.0 years ago by • 0
0
votes
0
replies
783
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
17 months ago Yijing • 0
1
vote
4
replies
1.7k
views
SingleR and gcc-8.3.0
gcc SingleR
updated 19 months ago by ▴ 20 • written 20 months ago by ▴ 10
0
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1
reply
1.0k
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 20 months ago by ▴ 740 • written 20 months ago by ▴ 10
0
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0
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654
views
input for singR function
Seurat_object singe-cell singleR
21 months ago Paria • 0
0
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1
reply
1.0k
views
SingleR error with multiple references
SingleR
updated 17 months ago by • 0 • written 24 months ago by • 0
1
vote
1
reply
921
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 24 months ago by ★ 4.5k • written 24 months ago by • 0
0
votes
1
reply
1.6k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 2.3 years ago by ★ 4.5k • written 2.3 years ago by • 0
0
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0
replies
1.2k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
2.3 years ago Guandong Shang ▴ 40
3
votes
4
replies
2.2k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
2.6 years ago • updated 2.5 years ago rohitsatyam102 ▴ 20
0
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1
reply
1.3k
views
celldex error when downloading reference datasets
celldex SingleR
updated 2.7 years ago by ★ 28k • written 2.7 years ago by • 0
15
votes
13
replies
3.6k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 3.0 years ago by ▴ 10 • written 3.0 years ago by ▴ 20
0
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1
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3.1k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 3.2 years ago by ★ 4.5k • written 3.2 years ago by • 0
0
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2
replies
4.2k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 2.6 years ago by • 0 • written 3.3 years ago by • 0
2
votes
3
replies
4.4k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
3.4 years ago • updated 3.3 years ago Imtiaz ▴ 10
2
votes
2
replies
3.1k
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 11 months ago by ★ 1.5k • written 3.5 years ago by ▴ 10
1
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1
reply
1.8k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR ImmgenData() mouseRNAseqData()
updated 3.7 years ago by ★ 6.6k • written 3.7 years ago by • 0
0
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1
reply
2.5k
views
SingleR and SCTransform
SingleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 20
2
votes
3
replies
1.9k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.9 years ago achaillon • 0
1
vote
5
replies
1.7k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 4.0 years ago by • 0 • written 4.1 years ago by ▴ 10
1
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1
reply
1.6k
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 4.1 years ago by ★ 28k • written 4.1 years ago by • 0
0
votes
6
replies
3.0k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 80
1
vote
3
replies
1.6k
views
Raw counts for reference dataset in single cell rnaseq
single cell celldex singleR
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 80
0
votes
2
replies
1.7k
views
most correlated genes in SingleR
singlecell singleR
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
0
votes
1
reply
1.8k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 4.2 years ago by ★ 28k • written 4.2 years ago by ▴ 50
0
votes
3
replies
2.3k
views
marker genes in singleR
singleR singlecell singlecellexperiment
updated 4.3 years ago by ★ 28k • written 4.3 years ago by ▴ 50
8
votes
16
replies
7.7k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 4.3 years ago by 4.1k • written 4.3 years ago by ▴ 660
0
votes
1
reply
1.4k
views
pheatmap needs to be manually added to plot heatmaps
singler bug
4.6 years ago muad.abdelhay ▴ 10
0
votes
1
reply
1.3k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR MouseGastrulationData
updated 4.6 years ago by ★ 28k • written 4.6 years ago by ▴ 70
2
votes
4
replies
1.5k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 4.8 years ago by ★ 28k • written 4.8 years ago by ▴ 120
1
vote
2
replies
1.8k
views
Error with cell annotation using singleR
SingleR
updated 4.8 years ago by ★ 13k • written 4.8 years ago by ▴ 10
42 results • Page 1 of 1
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Comment: How many of my genes from my gene list are in each KEGG pathway? by josephasmith1310 • 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open! by Esperan • 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom by Gordon Smyth 51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Comment: Adjusted p-values become NA when sub-setting samples by txema.heredia • 0
Thanks! I've been looking into DESeq2's code and, indeed, I get matching results when running manually the code inherited from the `genefi…
Answer: DESeq2 interaction between cancer cells and microenvironment cells by Michael Love 42k
I don't really know what you mean by "come from the contamination". You can look at the main effects and the interaction, but I don't know …
Votes
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
Answer: Consistent Decimals In Data After Antibody Array Background Correction Using Lim
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