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SingleR
•
reset
0
votes
2
replies
47k
views
SingleR Label.Ont
SingleR
written 17 months ago by
saeed.khalili
• 0
1
vote
1
reply
363
views
segfault when using singleR with Azimuth reference
SingleR
updated 4 months ago by
James W. MacDonald
68k • written 4 months ago by
Lluís Revilla Sancho
▴ 760
0
votes
1
reply
611
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
updated 6 months ago by
ATpoint
★ 4.7k • written 6 months ago by
nhaus
▴ 70
0
votes
1
reply
574
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 8 months ago by
ATpoint
★ 4.7k • written 8 months ago by
1319244258
• 0
0
votes
3
replies
1.2k
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 13 months ago by
Fayrouz
• 0
1
vote
2
replies
1.4k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR
SingleCellExperiment
14 months ago
elgomez
• 0
1
vote
4
replies
4.0k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
written 14 months ago by
Bine
▴ 50
2
votes
4
replies
3.0k
views
SingleR annotation of several slots/patients
SingleR
written 14 months ago by
Bine
▴ 50
0
votes
1
reply
562
views
SingleR Book Not Found
SingleR
updated 14 months ago by
Peter Hickey
▴ 750 • written 14 months ago by
jgattiker
• 0
1
vote
2
replies
2.0k
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 15 months ago by
ATpoint
★ 4.7k • written 15 months ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.6k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
19 months ago
Matvii Mykhailichenko
• 0
0
votes
4
replies
4.5k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 20 months ago by
Marco
• 0 • written 5.2 years ago by
mathai.c
• 0
0
votes
0
replies
877
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
20 months ago
Yijing
• 0
1
vote
4
replies
1.9k
views
SingleR and gcc-8.3.0
gcc
SingleR
updated 22 months ago by
Jovana Maksimovic
▴ 20 • written 23 months ago by
Fabien
▴ 10
0
votes
1
reply
1.2k
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 23 months ago by
Peter Hickey
▴ 750 • written 23 months ago by
cathalgking
▴ 10
0
votes
1
reply
922
views
input for singR function
Seurat_object
singe-cell
singleR
updated 15 days ago by
iamin053
• 0 • written 2.0 years ago by
Paria
• 0
0
votes
1
reply
1.1k
views
SingleR error with multiple references
SingleR
updated 21 months ago by
Irish
• 0 • written 2.2 years ago by
carlo
• 0
1
vote
1
reply
1.0k
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 2.3 years ago by
ATpoint
★ 4.7k • written 2.3 years ago by
mea2712
• 0
0
votes
1
reply
1.7k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 2.5 years ago by
ATpoint
★ 4.7k • written 2.5 years ago by
amit.korngut
• 0
0
votes
0
replies
1.4k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
2.6 years ago
Guandong Shang
▴ 40
3
votes
4
replies
2.4k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
2.8 years ago
rohitsatyam102
▴ 20
0
votes
1
reply
1.4k
views
celldex error when downloading reference datasets
celldex
SingleR
updated 3.0 years ago by
Aaron Lun
★ 28k • written 3.0 years ago by
indigofreesia
• 0
15
votes
13
replies
3.9k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 3.3 years ago by
xiang
▴ 10 • written 3.3 years ago by
immuno.dh
▴ 20
0
votes
1
reply
3.4k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment
SummarizedExperiment
SingleR
updated 3.5 years ago by
ATpoint
★ 4.7k • written 3.5 years ago by
Gen
• 0
0
votes
2
replies
4.5k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 2.9 years ago by
13304885395
• 0 • written 3.6 years ago by
ntourtillott23
• 0
2
votes
3
replies
4.9k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
3.7 years ago • updated 3.5 years ago
Imtiaz
▴ 10
2
votes
2
replies
3.4k
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 15 months ago by
Assa Yeroslaviz
★ 1.5k • written 3.8 years ago by
FantasticAI
▴ 10
1
vote
1
reply
2.0k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR
ImmgenData()
mouseRNAseqData()
updated 4.0 years ago by
Mike Smith
★ 6.6k • written 4.0 years ago by
Collins
• 0
0
votes
1
reply
2.8k
views
SingleR and SCTransform
SingleR
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
amel.zulji
▴ 20
2
votes
3
replies
2.0k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset
SingleR
SingleCellExperiment
4.2 years ago
achaillon
• 0
1
vote
5
replies
1.8k
views
SingleR Error in getMethod(generic, "ANY")
singleR
rowMedians
getMethod
updated 4.3 years ago by
bongowongo
• 0 • written 4.3 years ago by
inzirio
▴ 10
1
vote
1
reply
1.8k
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 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
w.gus.dunn
• 0
0
votes
6
replies
3.3k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
lirongrossmann
▴ 80
1
vote
3
replies
1.7k
views
Raw counts for reference dataset in single cell rnaseq
single cell
celldex
singleR
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
lirongrossmann
▴ 80
0
votes
2
replies
1.8k
views
most correlated genes in SingleR
singlecell
singleR
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
lirongrossmann
▴ 50
0
votes
1
reply
2.0k
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
lirongrossmann
▴ 50
0
votes
3
replies
2.5k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
lirongrossmann
▴ 50
8
votes
16
replies
8.3k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 4.5 years ago by
shepherl
4.1k • written 4.5 years ago by
enricoferrero
▴ 680
0
votes
1
reply
1.5k
views
pheatmap needs to be manually added to plot heatmaps
singler
bug
4.9 years ago
muad.abdelhay
▴ 10
0
votes
1
reply
1.4k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR
MouseGastrulationData
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
jma1991
▴ 70
2
votes
4
replies
1.7k
views
Impose minimum restrictions on correlations in SingleR
single cell
R
SingleR
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
k.vitting.seerup
▴ 120
1
vote
2
replies
2.0k
views
Error with cell annotation using singleR
SingleR
updated 5.1 years ago by
Steve Lianoglou
★ 13k • written 5.1 years ago by
bony.dekumar
▴ 10
42 results • Page
1 of 1
Recent ...
Replies
Comment: Weird p-values using DESeq2?
by
ATpoint
★ 4.7k
This does not look like normalized counts but raw counts. Consider using `counts(dds, normalized = TRUE)` or the output of `normTransform()…
Answer: Weird p-values using DESeq2?
by
Wolfgang Huber
★ 13k
Dear Ingrid, thank you for asking. Can you provide the input count matrix (you can "pseudonymize" the biological conditions and the gene n…
Comment: How to visualize these pathways using pathview
by
ingrid.h
• 0
Yes I have seen it, thanks.
Comment: Store Matrix in DataFrame Cell
by
Dario Strbenac
★ 1.6k
It does not appear to work. > DataFrame(name = "test", value = list(matrix(1:4, ncol = 2))) DataFrame with 2 rows and 3 columns …
Comment: Overcoming confounding in batch effect correction
by
Dario Strbenac
★ 1.6k
Actually, it is directly related. ComBat-seq is a part of [sva][1] package. It should use sva tag. [1]: https://bioconductor.org/package…
Votes
A: Fraction count for multi mapping reads; how to generate input file for Deseq2 fo
Comment: Weird p-values using DESeq2?
Comment: Overcoming confounding in batch effect correction
Answer: Store Matrix in DataFrame Cell
Answer: enrichGOgradient color change
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★ 13k
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68k
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16k
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shepherl
4.1k
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