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CellRanger
•
reset
0
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2
replies
217
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Non-empty droplets versus good quality cells
CellRanger
emptyDrops
scRNAseq
10X
7 weeks ago
rocanja
▴ 60
0
votes
0
replies
574
views
Read Cellranger outputs in R, combine as SingleCellExperiment
ReadInR
Cellranger
GEX+Features+VDJ
2.3 years ago
gregoire.destreel
• 0
0
votes
1
reply
980
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 2.0 years ago by
rohitsatyam102
▴ 20 • written 2.3 years ago by
gregoire.destreel
• 0
7
votes
12
replies
7.1k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
xingxd16
▴ 20
4 results • Page
1 of 1
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Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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