Showing : singleR • reset
0
votes
3
replies
455
views
dittobarplot Var error
RNASeq ditto dittoSeq SingleR
written 3 months ago by • 0
1
vote
2
replies
925
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR SingleCellExperiment
4 months ago elgomez • 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
2
votes
4
replies
1.2k
views
SingleR annotation of several slots/patients
SingleR
written 4 months ago by ▴ 40
0
votes
1
reply
302
views
SingleR Book Not Found
SingleR
updated 4 months ago by ▴ 740 • written 4 months ago by • 0
1
vote
2
replies
733
views
trying to add SingleR label to Seurat Object fails
SingleR Seurat
updated 5 months ago by ★ 4.0k • written 5 months ago by ★ 1.5k
0
votes
4
replies
3.9k
views
SingleR Label.Ont
SingleR
updated 9 days ago by • 0 • written 7 months ago by • 0
0
votes
2
replies
885
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR SingleCellExperiment SingleCellData
10 months ago Matvii Mykhailichenko • 0
0
votes
0
replies
523
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
10 months ago Yijing • 0
0
votes
1
reply
718
views
scRNAseq package and cell type annotations
ExperimentHub R ExperimentHubData scRNAseq SingleR
updated 13 months ago by ▴ 740 • written 13 months ago by ▴ 10
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
0
replies
469
views
input for singR function
Seurat_object singe-cell singleR
14 months ago Paria • 0
0
votes
1
reply
779
views
SingleR error with multiple references
SingleR
updated 11 months ago by • 0 • written 17 months ago by • 0
1
vote
1
reply
708
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 17 months ago by ★ 4.0k • written 17 months ago by • 0
0
votes
1
reply
1.0k
views
Error in running: classifySingleR from SingleR package
SingleR SingleCell
updated 21 months ago by ★ 4.0k • written 21 months ago by • 0
0
votes
0
replies
951
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR scRNAseq
21 months ago Guandong Shang ▴ 40
3
votes
4
replies
1.7k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
2.0 years ago • updated 23 months ago rohitsatyam102 ▴ 20
0
votes
1
reply
927
views
celldex error when downloading reference datasets
celldex SingleR
updated 2.2 years ago by ★ 28k • written 2.2 years ago by • 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
1
reply
2.6k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment SummarizedExperiment SingleR
updated 2.7 years ago by ★ 4.0k • written 2.7 years ago by • 0
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
2
votes
3
replies
3.6k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
2.8 years ago • updated 2.7 years ago Imtiaz ▴ 10
2
votes
2
replies
2.5k
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
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
0
votes
1
reply
1.9k
views
SingleR and SCTransform
SingleR
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 20
1
vote
3
replies
1.5k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset SingleR SingleCellExperiment
3.4 years ago • updated 3.3 years ago achaillon • 0
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
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
0
votes
6
replies
2.6k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell singlecellexperiment umap singleR
updated 3.6 years ago by ★ 28k • written 3.6 years ago by ▴ 80
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
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
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
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
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
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
997
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
2
votes
4
replies
1.3k
views
Impose minimum restrictions on correlations in SingleR
single cell R SingleR
updated 4.2 years ago by ★ 28k • written 4.3 years ago by ▴ 120
1
vote
2
replies
1.5k
views
Error with cell annotation using singleR
SingleR
updated 4.3 years ago by ★ 13k • written 4.3 years 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
39 results • Page 1 of 1
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Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Comment: PCA plot suggestions by JKim • 0
cross post: https://www.biostars.org/p/9593486/
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
You cannot correct for technical variability due to batch if samples are nested in batch. The technical and biological differences are comp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2) by James W. MacDonald 65k
You will need to show some reproducible code for anybody to track this down. Please note that `DESeq2` has been used by thousands of people…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
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