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singleR
•
reset
0
votes
0
replies
24
views
input for singR function
Seurat_object
singe-cell
singleR
2 days ago
Paria
• 0
0
votes
0
replies
107
views
SingleR error with multiple references
SingleR
11 weeks ago
carlo
• 0
1
vote
1
reply
111
views
SingleR using TPM in a bulk RNA seq dataset
SingleR
updated 12 weeks ago by
ATpoint
★ 2.1k • written 12 weeks ago by
mea2712
• 0
0
votes
1
reply
290
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
188
views
how to calculate similarity between each cluster in scRNA and bulk RNA-seq
SingleR
scRNAseq
6 months ago
Guandong Shang
▴ 40
3
votes
4
replies
664
views
Using SingleR for Single cell annotation with BulkRNASeq
SingleR
9 months ago • updated 8 months ago
rohitsatyam102
▴ 20
0
votes
1
reply
331
views
celldex error when downloading reference datasets
celldex
SingleR
updated 11 months ago by
Aaron Lun
★ 28k • written 11 months ago by
indigofreesia
• 0
15
votes
13
replies
1.5k
views
celldex ensembl gene annotation issue
SingleR
celldex
HumanPrimaryCellAtlasData
ensembl
updated 14 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
883
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
1.0k
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
764
views
SingleCellExperiment and SingleR for identifying T cell subsets
cellsubset
SingleR
SingleCellExperiment
2.1 years ago
achaillon
• 0
1
vote
5
replies
976
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
686
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 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
w.gus.dunn
• 0
0
votes
6
replies
1.2k
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
623
views
Raw counts for reference dataset in single cell rnaseq
single cell
celldex
singleR
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
lirongrossmann
▴ 70
0
votes
2
replies
781
views
most correlated genes in SingleR
singlecell
singleR
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
lirongrossmann
▴ 40
0
votes
1
reply
624
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
592
views
pheatmap needs to be manually added to plot heatmaps
singler
bug
2.8 years ago
muad.abdelhay
▴ 10
0
votes
1
reply
471
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
584
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
832
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
Answer: struggling to create a heatmap
by
ATpoint
★ 2.1k
I am reluctant to read through that wall of code. Here is what would work. Note that prefiltering makes sense before, not after running `DE…
Answer: collapseReplicates error after tximeta
by
Michael Love
39k
The issue is that `collapseReplicates` just collapses `counts` and doesn't account for multiple assays which you need for e.g. Swish or oth…
Comment: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
by
ATpoint
★ 2.1k
That having said, I recommend to inspect the MA-plots (`plotMA()`), at best the ones produced right from `res <- results(dds); plotMA(res)`…
Answer: Which genes are outliers in DESeq2?
by
ATpoint
★ 2.1k
You can take over some of the lines from `results()` to find them easily: ```r suppressPackageStartupMessages(library(DESeq2)) set.s…
Answer: Which genes are outliers in DESeq2?
by
Michael Love
39k
Outliers will have high maxCooks values in `mcols(dds)` -- the threshold is `qf(.99, p, n - p)` where n is sample size and p is number of c…
Votes
Significant reporter activity with mpralm function
Answer: I cannot install annotables package in Rstudio (macOS)
Answer: log2 of normalized counts for further analyzes
Answer: Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it
Clarification of what DESeq2::estimateSizeFactors controlGenes does and when it should *not* be used
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Guido Hooiveld
★ 3.5k
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to
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62k
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Michael Love
39k
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twtoal
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