Showing : SingleR • reset
15
votes
13
replies
3.0k
views
celldex ensembl gene annotation issue
SingleR celldex HumanPrimaryCellAtlasData ensembl
updated 2.5 years ago by ▴ 10 • written 2.5 years ago by ▴ 20
8
votes
16
replies
6.2k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.7 years ago by 3.9k • written 3.7 years ago by ▴ 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 ★ 1.5k • written 3.0 years ago by ▴ 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 ★ 28k • written 4.3 years ago by ▴ 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 ▴ 40
1
vote
5
replies
1.5k
views
SingleR Error in getMethod(generic, "ANY")
singleR rowMedians getMethod
updated 3.5 years ago by • 0 • written 3.5 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Error with cell annotation using singleR
SingleR
updated 4.3 years ago by ★ 13k • written 4.3 years ago by ▴ 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 ★ 28k • written 3.7 years ago by ▴ 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 ★ 28k • written 3.6 years ago by • 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 ★ 6.5k • written 3.2 years ago by • 0
1
vote
1
reply
722
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 18 months ago by ★ 4.1k • written 18 months ago by • 0
1
vote
2
replies
935
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
769
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 5 months ago by ★ 4.1k • written 5 months ago by ★ 1.5k
1
vote
4
replies
1.2k
views
SingleR and gcc-8.3.0
gcc SingleR
updated 13 months ago by ▴ 10 • written 13 months ago by ▴ 10
1
vote
4
replies
1.7k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 4 months ago by ▴ 40
0
votes
1
reply
1.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.1k • written 21 months ago by • 0
0
votes
1
reply
2.6k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.1k • written 2.7 years ago by • 0
0
votes
1
reply
315
views
SingleR Book Not Found
SingleR
updated 5 months ago by ▴ 740 • written 5 months ago by • 0
0
votes
1
reply
730
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
0
votes
2
replies
3.6k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 2.1 years ago by • 0 • written 2.8 years ago by • 0
0
votes
0
replies
529
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
11 months ago Yijing • 0
0
votes
0
replies
475
views
input for singR function
Seurat_object singe-cell singleR
15 months ago Paria • 0
0
votes
3
replies
481
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
0
votes
0
replies
965
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 • 0 • written 4.4 years ago by • 0
0
votes
2
replies
901
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 ★ 28k • written 3.7 years ago by ▴ 40
0
votes
2
replies
1.5k
views
most correlated genes in SingleR
singlecell singleR
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
0
votes
4
replies
5.4k
views
SingleR Label.Ont
SingleR
updated 18 days ago by • 0 • written 7 months ago by • 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 ★ 28k • written 3.7 years ago by ▴ 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
787
views
SingleR error with multiple references
SingleR
updated 11 months ago by • 0 • written 17 months ago by • 0
0
votes
1
reply
2.0k
views
SingleR and SCTransform
SingleR
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 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 ★ 28k • written 4.1 years ago by ▴ 70
0
votes
1
reply
945
views
celldex error when downloading reference datasets
celldex SingleR
updated 2.2 years ago by ★ 28k • written 2.2 years ago by • 0
0
votes
1
reply
1.4k
views
predicting cell type of clusters using singleR
singleR singlecell
updated 3.7 years ago by ★ 28k • written 3.7 years ago by ▴ 40
39 results • Page 1 of 1
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Answer: limma Intercept vs No-intercept models completely changing DMR results? by Gordon Smyth 50k
I'll add a little bit of general advice to James' answer. You seem to have the misunderstanding that you can change the design matrix but …
Answer: package goseq seems to be not available on the latest version of R by Gordon Smyth 50k
It is true that goseq isn't available for Bioc 3.19. That is because goseq depends on txbmaker, which is itself not yet available for Bioc…
Answer: limma Intercept vs No-intercept models completely changing DMR results? by James W. MacDonald 65k
This part: ``` design_intercept <- model.matrix(~Alt+Sex+Age+PC1, data=targets_Sherpa) colnames(design_intercept) <- c("AltSHP_LA","Al…
Comment: CombineArrays for EPIC and EPIC V2 by Kim • 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga by Michael Love 41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Votes
Answer: limma Intercept vs No-intercept models completely changing DMR results?
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
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