Showing : SingleR • reset
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
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
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
1
reply
1000
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
8
votes
16
replies
6.2k
views
Cannot connect to ExperimentHub server
ExperimentHub AnnotationHub SingleR
updated 3.7 years ago by 3.8k • written 3.7 years ago by ▴ 660
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
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
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
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
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
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
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
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
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
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
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
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
3
replies
471
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
1
vote
2
replies
747
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
0
votes
2
replies
893
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
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
0
votes
4
replies
4.8k
views
SingleR Label.Ont
SingleR
updated 14 days ago by • 0 • written 7 months ago by • 0
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
0
votes
1
reply
723
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
2
votes
4
replies
1.3k
views
SingleR annotation of several slots/patients
SingleR
written 4 months ago by ▴ 40
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
311
views
SingleR Book Not Found
SingleR
updated 5 months ago by ▴ 740 • written 5 months ago by • 0
1
vote
2
replies
931
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
4 months ago elgomez • 0
1
vote
1
reply
715
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 17 months ago by ★ 4.1k • written 17 months ago by • 0
0
votes
1
reply
937
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
0
replies
956
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
22 months ago Guandong Shang ▴ 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
1
vote
4
replies
1.6k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR SeuratscRNA
written 4 months ago by ▴ 40
0
votes
0
replies
527
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
10 months ago Yijing • 0
0
votes
0
replies
472
views
input for singR function
Seurat_object singe-cell singleR
15 months ago Paria • 0
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
782
views
SingleR error with multiple references
SingleR
updated 11 months ago by • 0 • written 17 months ago by • 0
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Comment: putting my own expression data in deseq2 by ATpoint ★ 4.1k
> directly from GEOquery I can tell you that GEOquery retrieves array data not appropriate for DESeq2. For anything else make your questi…
Comment: Assist me in determining whether the analysis process using the limma package ha by SSSJec • 0
Thanks for your reply. I understand the principle of adjusted P-values, but I still want to address that issue. The description of the G…
Comment: Why p value inconsistent when using different number of pathway score? by Gordon Smyth 50k
Just a note that fgsea is not classical GSEA. The classical GSEA as described in the Subramanian paper and other papers from the Broad Inst…
Comment: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by Chris • 0
Thank you! The resource I use may mispresent the requirement input of fgsea.
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha by alserg ▴ 260
fgsea doesn't require the presence of deferentially expressed genes, it takes as the input the differential expression-based ranking of all…
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Nominations for Bioconductor Awards 2024!
Answer: Improving the design matrices vignette in RNAseq123
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Answer: Perform gene set enrichment analysis using fgsea on two conditions that don't ha
Comment: DESeq2: Contrast for two conditions combined versus one condition (A+B_vs_C)
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