Showing : DropletUtils • reset
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 ★ 28k • written 5.2 years ago by ▴ 20
0
votes
8
replies
1.6k
views
DropletUtils::read10xCounts error
read10xCounts DropletUtils
16 months ago • updated 15 months ago fdumetz • 0
3
votes
8
replies
915
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils droplet
written 5 months ago by ▴ 10
0
votes
7
replies
1.5k
views
DropletUtils::swappedDrops more cells than using Read10x with filtered_feature_bc_matrix files
10x genomics DropletUtils single cell RNA seq
updated 4.2 years ago by ★ 28k • written 4.2 years ago by • 0
1
vote
6
replies
1.4k
views
DropletUtils::swappedDrops segfault memory not mapped
DropletUtils
3.0 years ago • updated 2.9 years ago wesselyf • 0
1
vote
5
replies
1.2k
views
about DropletUtils and scRNA-seq
dropseq dropletutils droplet
updated 5.3 years ago by ★ 28k • written 5.3 years ago by ▴ 670
2
votes
5
replies
1.2k
views
Recommendations for running DropletUtils::swappedDrops() on multiplexed samples from multiple libraries
dropletutils swappeddrops
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
4
votes
5
replies
2.0k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils scRNA-seq emptyDrops simplesinglecell cell calling
updated 3.5 years ago by ★ 28k • written 4.7 years ago by ▴ 140
4
votes
5
replies
2.3k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
21 months ago • updated 20 months ago Peter Hickey ▴ 740
2
votes
4
replies
1.3k
views
Error when reading data with DropletUtils::read10xCounts
DropletUtils
updated 5.9 years ago by ★ 28k • written 5.9 years ago by • 0
0
votes
4
replies
1.8k
views
Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into DropletUtils
DropletUtils h5
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 350
1
vote
4
replies
988
views
Is there a limitation to the number of cells swappedDrops can handle?
swappedDrops DropletUtils
5.0 years ago joseph.joonsang • 0
0
votes
4
replies
1.0k
views
DropletUtils' emptyDrops() fails with non-integer counts
DropletUtils
updated 4.7 years ago by ★ 28k • written 4.7 years ago by • 0
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils scRNAseq
updated 3.2 years ago by ★ 28k • written 3.2 years ago by ▴ 740
0
votes
3
replies
1.2k
views
Running DropletUtils::swappedDrops() on multiplexed samples from different libraries
swappeddrops dropletutils
updated 4.5 years ago by ★ 28k • written 4.5 years ago by • 0
1
vote
3
replies
1.9k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment DropletUtils SingleCellData
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 10
0
votes
3
replies
693
views
insufficient unique points for computing knee/inflection points
DropletUtils SingleCellData
updated 9 months ago by ★ 4.1k • written 9 months ago by • 0
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils SingleCellExperiement DelayedArray simpleSingleCell
updated 4.9 years ago by ★ 28k • written 4.9 years ago by ▴ 170
1
vote
2
replies
921
views
In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
dropletutils
updated 5.1 years ago by ▴ 20 • written 5.1 years ago by ▴ 70
2
votes
2
replies
1.1k
views
What`s new features in DropletUtils version 1.3.10 comapred to version 1.2.2
DropletUtils Bioconductor singel cell
updated 5.2 years ago by ★ 28k • written 5.2 years ago by ▴ 20
3
votes
2
replies
967
views
Should we apply DropletUtils on control case separately or on a common sce object.
DropletUtils
3.0 years ago rohitsatyam102 ▴ 20
0
votes
2
replies
1.1k
views
DropletUtils barcodeRanks bug (?)
dropletutils
updated 5.4 years ago by ★ 28k • written 5.4 years ago by • 0
1
vote
2
replies
1.3k
views
Segmentation Fault with development versions of R, Bioconductor, and DropletUtils when processing output of CellRanger 3.0.2
DropletUtils Bioc-devel
5.1 years ago Matthew Thornton ▴ 350
7
votes
2
replies
2.4k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment dropletutils simplesinglecell
updated 5.6 years ago by ★ 28k • written 5.6 years ago by ▴ 740
0
votes
2
replies
1.0k
views
Scalability of emptyDrops() running times
dropletutils emptydrops
updated 5.0 years ago by ★ 28k • written 5.0 years ago by • 0
0
votes
1
reply
1.0k
views
Can DropletUtils Package be used to identify cells for 10X VDJ data ?
DropletUtils 10X 5` TCR single cells
updated 5.1 years ago by ★ 28k • written 5.1 years ago by ▴ 20
5
votes
1
reply
4.5k
views
Error with DropletUtils::EmptyDrops()
DropletUtils EmptyDrops simpleSingleCell
updated 21 months ago by ▴ 10 • written 4.8 years ago by ▴ 20
0
votes
1
reply
786
views
DropletUtils::swappedDrops - Kallisto instead of CellRanger?
DropletUtils
updated 3.4 years ago by ★ 28k • written 3.4 years ago by • 0
1
vote
1
reply
1.0k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils emptyDrops 10x
updated 3.3 years ago by ★ 28k • written 3.3 years ago by ▴ 740
0
votes
1
reply
838
views
emptyDrops result is full NAs
scran dropletUtils scater scRNA-Seq
4.9 years ago hamza_karakurt ▴ 50
0
votes
1
reply
980
views
Aberrant number of cells
CellBarcode DropletUtils emptyDrops() Cellranger scRNAseq
updated 2.0 years ago by ▴ 20 • written 2.3 years ago by • 0
3
votes
1
reply
686
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
updated 6 months ago by ★ 4.1k • written 19 months ago by ★ 1.5k
0
votes
1
reply
879
views
Using controlAmbience with multiple samples and conditions
DropletUtils
updated 2.3 years ago by ★ 28k • written 2.4 years ago by ▴ 70
1
vote
1
reply
662
views
Input format for `combinations` in `hashedDrops`
DropletUtils
updated 2.3 years ago by ★ 28k • written 2.3 years ago by ▴ 270
2
votes
1
reply
1.0k
views
barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df, ...)"
DropletUtils
updated 3.0 years ago by ★ 28k • written 3.0 years ago by ▴ 20
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Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by Gordon Smyth 50k
Regardless of whether it agrees with `t.test` or not, the formula given in the original question is correct and is more accurate than the f…
Comment: Limma without eBayes, is it indistunguishable from Ordinary Least Square? by nbay13 • 0
A little late to the party, but I found that using the equation you specified, the p-values are actually slightly off from base R's `t.test…
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)`)?
Answer: Extremely small p-values using Limma for proteomic data by James W. MacDonald 65k
If you fit a cell means model (without an intercept), you will have to construct contrasts using `makeContrasts` and fit them using `contra…
Votes
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
Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
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