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SingleR
•
reset
0
votes
0
replies
33
views
input for singR function
Seurat_object
singe-cell
singleR
7 days ago
Paria
• 0
0
votes
0
replies
113
views
SingleR error with multiple references
SingleR
11 weeks ago
carlo
• 0
1
vote
1
reply
124
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 3 months ago by
ATpoint
★ 2.1k • written 3 months ago by
mea2712
• 0
0
votes
1
reply
302
views
Error in running: classifySingleR from SingleR package
SingleR
SingleCell
updated 6 months ago by
ATpoint
★ 2.1k • written 6 months ago by
amit.korngut
• 0
0
votes
0
replies
195
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
7 months ago
Guandong Shang
▴ 40
3
votes
4
replies
674
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
10 months ago • updated 9 months ago
rohitsatyam102
▴ 20
0
votes
1
reply
334
views
celldex error when downloading reference datasets
celldex
SingleR
updated 11 months ago by
Aaron Lun
★ 28k • written 12 months ago by
indigofreesia
• 0
15
votes
13
replies
1.5k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 15 months ago by
xiang
▴ 10 • written 15 months ago by
immuno.dh
▴ 20
0
votes
1
reply
1.2k
views
Convert SummarizedExperiment to SingleCellExperiment Object
SingleCellExperiment
SummarizedExperiment
SingleR
updated 17 months ago by
ATpoint
★ 2.1k • written 17 months ago by
Gen
• 0
0
votes
2
replies
1.7k
views
Single R-- Error in is.null(rownames(x)) && nrow(x) : invalid 'y' type in 'x && y'
SingleR
updated 10 months ago by
13304885395
• 0 • written 19 months ago by
ntourtillott23
• 0
2
votes
3
replies
1.6k
views
Error in SingleR, no common genes between 'test' and 'ref'
SingleR
19 months ago • updated 18 months ago
Imtiaz
▴ 10
1
vote
2
replies
1.2k
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 21 months ago by
Aaron Lun
★ 28k • written 21 months ago by
FantasticAI
• 0
1
vote
1
reply
898
views
SingleR::mouseRNAseqData Error in UseMethod(filter_)
SingleR
ImmgenData()
mouseRNAseqData()
updated 23 months ago by
Mike Smith
★ 5.9k • written 23 months ago by
Collins
• 0
0
votes
1
reply
1.1k
views
SingleR and SCTransform
SingleR
updated 24 months ago by
Aaron Lun
★ 28k • written 24 months ago by
amel.zulji
▴ 20
1
vote
3
replies
777
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset
SingleR
SingleCellExperiment
2.2 years ago • updated 2.1 years ago
achaillon
• 0
1
vote
5
replies
982
views
SingleR Error in getMethod(generic, "ANY")
singleR
rowMedians
getMethod
updated 2.3 years ago by
bongowongo
• 0 • written 2.3 years ago by
inzirio
▴ 10
1
vote
1
reply
690
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 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
w.gus.dunn
• 0
0
votes
6
replies
1.3k
views
Discrepancy between cell type and cluster using SingleCellExperiment and SingleR
singlecell
singlecellexperiment
umap
singleR
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
lirongrossmann
▴ 70
1
vote
3
replies
630
views
Raw counts for reference dataset in single cell rnaseq
single cell
celldex
singleR
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
lirongrossmann
▴ 70
0
votes
2
replies
786
views
most correlated genes in SingleR
singlecell
singleR
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
lirongrossmann
▴ 40
0
votes
1
reply
631
views
predicting cell type of clusters using singleR
singleR
singlecell
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
lirongrossmann
▴ 40
0
votes
3
replies
1.2k
views
marker genes in singleR
singleR
singlecell
singlecellexperiment
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
lirongrossmann
▴ 40
8
votes
16
replies
2.5k
views
Cannot connect to ExperimentHub server
ExperimentHub
AnnotationHub
SingleR
updated 2.5 years ago by
shepherl
3.4k • written 2.5 years ago by
enricoferrero
▴ 650
0
votes
1
reply
599
views
pheatmap needs to be manually added to plot heatmaps
singler
bug
2.8 years ago
muad.abdelhay
▴ 10
0
votes
1
reply
476
views
Assay choice for cell type annotation using SingleR when batch effect present in profile
SingleR
MouseGastrulationData
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
jma1991
▴ 70
2
votes
4
replies
589
views
Impose minimum restrictions on correlations in SingleR
single cell
R
SingleR
updated 3.0 years ago by
Aaron Lun
★ 28k • written 3.0 years ago by
k.vitting.seerup
▴ 120
1
vote
2
replies
841
views
Error with cell annotation using singleR
SingleR
updated 3.1 years ago by
Steve Lianoglou
13k • written 3.1 years ago by
bony.dekumar
• 0
0
votes
3
replies
2.0k
views
error in (function (classes, fdef, mtable) unable to find an inherited method for function logNormCounts for signature Seurat
seurat
singleR
updated 3.2 years ago by
Gordon Smyth
47k • written 3.2 years ago by
mathai.c
• 0
28 results • Page
1 of 1
Recent ...
Replies
Comment: DESeq2 and heatmap for multiple comparisons
by
artem.vorobyev
• 0
this I already did. My question is how to visualize differentially expressed genes on the heatmap for all 3 groups (healty->lesion->treat…
Comment: athPkgBuilder data source :missing probesets
by
nicklesteele532
• 0
> >>> > >>> How to handle the one probeset to multiple locus mappings? I can > >think 3 > >>> possible solutions: > >>> 1. pick the "best" …
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
> sum(width(gr_toexclude)) [1] 2713499861 I excluded everything which was not locus. If small rna locus is from 2000 to 4000 and next locu…
Comment: Why in Bioconductor community people rarely upvote questions?
by
Hervé Pagès
16k
BTW I fail to see how the lack of upvotes to a question would be discouraging as long as you get a good answer. OTOH I can see how failing …
Answer: DESeq2 and heatmap for multiple comparisons
by
swbarnes2
★ 1.2k
If you want to know what genes are different between lesion and treated, compare them to each other.
Votes
Comment: recount 3 protect read length metadata
Answer: Doubts about manipulation and annotation of microarray files deposited at GEO
C: Batch correction in DESeq2
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
Comment: Strand information in a GAlignmentsList object derived from strand-specific pair
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Chris
• 0
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to
Malcolm Cook
★ 1.6k
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to
Hervé Pagès
16k
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to
Hans-Ulrich Klein
▴ 330
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JoeMG
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