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SingleR
•
reset
0
votes
0
replies
70
views
Validity of SingleR with very small bulk RNAseq reference
SingleR
16 hours ago
nhaus
▴ 50
0
votes
8
replies
27k
views
SingleR Label.Ont
SingleR
written 10 months ago by
saeed.khalili
• 0
0
votes
1
reply
361
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 6 weeks ago by
ATpoint
★ 4.2k • written 6 weeks ago by
1319244258
• 0
0
votes
3
replies
746
views
dittobarplot Var error
RNASeq
ditto
dittoSeq
SingleR
written 6 months ago by
Fayrouz
• 0
1
vote
2
replies
1.1k
views
Reduce single cell experiment size to use as reference for annotation with SingleR
SingleR
SingleCellExperiment
7 months ago
elgomez
• 0
1
vote
4
replies
2.4k
views
JoinLayers function for Seurat Object for annotation with SingleR
SingleR
SeuratscRNA
written 7 months ago by
Bine
▴ 50
2
votes
4
replies
1.9k
views
SingleR annotation of several slots/patients
SingleR
written 7 months ago by
Bine
▴ 50
0
votes
1
reply
401
views
SingleR Book Not Found
SingleR
updated 8 months ago by
Peter Hickey
▴ 740 • written 8 months ago by
jgattiker
• 0
1
vote
2
replies
1.1k
views
trying to add SingleR label to Seurat Object fails
SingleR
Seurat
updated 8 months ago by
ATpoint
★ 4.2k • written 8 months ago by
Assa Yeroslaviz
★ 1.5k
0
votes
2
replies
1.1k
views
Error in SingleR, no common genes between 'test' and 'ref'
singleR
SingleCellExperiment
SingleCellData
13 months ago
Matvii Mykhailichenko
• 0
0
votes
4
replies
3.9k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 13 months ago by
Marco
• 0 • written 4.7 years ago by
mathai.c
• 0
0
votes
0
replies
652
views
what should be the input for SingleR() automatic cell type annotation?
SingleR
13 months ago
Yijing
• 0
1
vote
4
replies
1.4k
views
SingleR and gcc-8.3.0
gcc
SingleR
updated 16 months ago by
Jovana Maksimovic
▴ 10 • written 16 months ago by
Fabien
▴ 10
0
votes
1
reply
878
views
scRNAseq package and cell type annotations
ExperimentHub
R
ExperimentHubData
scRNAseq
SingleR
updated 16 months ago by
Peter Hickey
▴ 740 • written 16 months ago by
cathalgking
▴ 10
0
votes
0
replies
548
views
input for singR function
Seurat_object
singe-cell
singleR
18 months ago
Paria
• 0
0
votes
1
reply
905
views
SingleR error with multiple references
SingleR
updated 14 months ago by
Irish
• 0 • written 20 months ago by
carlo
• 0
1
vote
1
reply
810
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 20 months ago by
ATpoint
★ 4.2k • written 20 months ago by
mea2712
• 0
0
votes
1
reply
1.4k
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 24 months ago by
ATpoint
★ 4.2k • written 24 months ago by
amit.korngut
• 0
0
votes
0
replies
1.1k
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
2.0 years ago
Guandong Shang
▴ 40
3
votes
4
replies
2.0k
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
2.3 years ago • updated 2.2 years ago
rohitsatyam102
▴ 20
0
votes
1
reply
1.1k
views
celldex error when downloading reference datasets
celldex
SingleR
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
indigofreesia
• 0
15
votes
13
replies
3.3k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 2.7 years ago by
xiang
▴ 10 • written 2.7 years ago by
immuno.dh
▴ 20
0
votes
1
reply
2.9k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment
SummarizedExperiment
SingleR
updated 2.9 years ago by
ATpoint
★ 4.2k • written 2.9 years ago by
Gen
• 0
0
votes
2
replies
3.9k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 2.4 years ago by
13304885395
• 0 • written 3.0 years ago by
ntourtillott23
• 0
2
votes
3
replies
4.0k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
3.1 years ago • updated 3.0 years ago
Imtiaz
▴ 10
2
votes
2
replies
2.9k
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 8 months ago by
Assa Yeroslaviz
★ 1.5k • written 3.2 years ago by
FantasticAI
▴ 10
1
vote
1
reply
1.7k
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR
ImmgenData()
mouseRNAseqData()
updated 3.4 years ago by
Mike Smith
★ 6.5k • written 3.4 years ago by
Collins
• 0
0
votes
1
reply
2.2k
views
SingleR and SCTransform
SingleR
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
amel.zulji
▴ 20
2
votes
3
replies
1.7k
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset
SingleR
SingleCellExperiment
3.6 years ago
achaillon
• 0
1
vote
5
replies
1.6k
views
SingleR Error in getMethod(generic, "ANY")
singleR
rowMedians
getMethod
updated 3.8 years ago by
bongowongo
• 0 • written 3.8 years ago by
inzirio
▴ 10
1
vote
1
reply
1.4k
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 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
w.gus.dunn
• 0
0
votes
6
replies
2.8k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lirongrossmann
▴ 80
1
vote
3
replies
1.4k
views
Raw counts for reference dataset in single cell rnaseq
single cell
celldex
singleR
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lirongrossmann
▴ 80
0
votes
2
replies
1.6k
views
most correlated genes in SingleR
singlecell
singleR
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
lirongrossmann
▴ 50
0
votes
1
reply
1.6k
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
lirongrossmann
▴ 50
0
votes
3
replies
2.1k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
lirongrossmann
▴ 50
8
votes
16
replies
6.8k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 4.0 years ago by
shepherl
3.9k • written 4.0 years ago by
enricoferrero
▴ 660
0
votes
1
reply
1.3k
views
pheatmap needs to be manually added to plot heatmaps
singler
bug
4.3 years ago
muad.abdelhay
▴ 10
0
votes
1
reply
1.1k
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR
MouseGastrulationData
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
jma1991
▴ 70
2
votes
4
replies
1.4k
views
Impose minimum restrictions on correlations in SingleR
single cell
R
SingleR
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
k.vitting.seerup
▴ 120
1
vote
2
replies
1.7k
views
Error with cell annotation using singleR
SingleR
updated 4.6 years ago by
Steve Lianoglou
★ 13k • written 4.6 years ago by
bony.dekumar
▴ 10
41 results • Page
1 of 1
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Replies
Comment: 'path' must be string
by
James W. MacDonald
66k
Yes. We already knew that from the error message, and I told you that in my previous email. The point wasn't to figure out *where* the err…
Comment: 'path' must be string
by
cpierce2
• 0
I ran the debugger and this is the line that causes the error: ``` if (any(startsWith(pkcData[["RTS_ID"]][1L], "RTS")) & any(startsWith(pr…
Comment: Generating surrogate variables across multiple variables of interest
by
Robert
• 0
Yes, we have several biomarkers, and a proteomic set, so we are characterizing each biomarker by it's proteomic association(s). The use for…
Comment: Error running tximeta
by
Guido Hooiveld
★ 4.0k
FYI (since I just finalized a run with `salmon`). For each sample (`.`) an output folder is created that contains 3 files (`cmd_info.json`…
Comment: Error running tximeta
by
Michael Love
42k
Tximeta uses the full directory. There are files that give the key information about the transcriptome. It's not a good idea to selectively…
Votes
Question: Deconvolution Methods on RNA-Seq Data (Mixed cell types)
Answer: Understanding how to contrast two treatments in DESeq2
Answer: Understanding how to contrast two treatments in DESeq2
Cannot extract TxFeatures for a defined GRanges object
Limma time series spline help
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Lluís Revilla Sancho
▴ 730
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to
maltethodberg
▴ 180
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to
Michael Love
42k
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to
Leonardo Collado Torres
★ 1.1k
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to
Gordon Smyth
51k
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