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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
Aaron Lun
★ 28k • written 5.2 years ago by
xingxd16
▴ 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
920
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 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
Aaron Lun
★ 28k • written 4.2 years ago by
gil.stelzer
• 0
1
vote
6
replies
1.4k
views
DropletUtils::swappedDrops segfault memory not mapped
DropletUtils
3.0 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
Aaron Lun
★ 28k • written 5.3 years ago by
Bogdan
▴ 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
Aaron Lun
★ 28k • written 5.0 years ago by
rosano
• 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
Aaron Lun
★ 28k • written 4.7 years ago by
C T
▴ 140
4
votes
5
replies
2.4k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
21 months ago
Peter Hickey
▴ 740
2
votes
4
replies
1.3k
views
Error when reading data with DropletUtils::read10xCounts
DropletUtils
updated 6.0 years ago by
Aaron Lun
★ 28k • written 6.0 years ago by
fabrost
• 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
Aaron Lun
★ 28k • written 5.1 years ago by
Matthew Thornton
▴ 350
1
vote
4
replies
990
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
Aaron Lun
★ 28k • written 4.7 years ago by
jmanning
• 0
2
votes
4
replies
1.2k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
Peter Hickey
▴ 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
Aaron Lun
★ 28k • written 4.5 years ago by
rosano
• 0
1
vote
3
replies
1.9k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
msn
▴ 10
0
votes
3
replies
697
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 9 months ago by
ATpoint
★ 4.1k • written 9 months ago by
p.vlachou-efstathiou
• 0
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
Steve Pederson
▴ 170
1
vote
2
replies
922
views
In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
dropletutils
updated 5.1 years ago by
s1437643
▴ 20 • written 5.1 years ago by
jma1991
▴ 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
Aaron Lun
★ 28k • written 5.2 years ago by
xingxd16
▴ 20
3
votes
2
replies
968
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
Aaron Lun
★ 28k • written 5.4 years ago by
jmanning
• 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
Aaron Lun
★ 28k • written 5.6 years ago by
Peter Hickey
▴ 740
0
votes
2
replies
1.0k
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
rosano
• 0
0
votes
1
reply
1.1k
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
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
5
votes
1
reply
4.5k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 21 months ago by
Stefano Mangiola
▴ 10 • written 4.8 years ago by
shbrief
▴ 20
0
votes
1
reply
786
views
DropletUtils::swappedDrops - Kallisto instead of CellRanger?
DropletUtils
updated 3.4 years ago by
Aaron Lun
★ 28k • written 3.4 years ago by
mhalache
• 0
1
vote
1
reply
1.1k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 3.3 years ago by
Aaron Lun
★ 28k • written 3.3 years ago by
Peter Hickey
▴ 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
981
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
3
votes
1
reply
689
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
updated 6 months ago by
ATpoint
★ 4.1k • written 19 months ago by
Dario Strbenac
★ 1.5k
0
votes
1
reply
880
views
Using controlAmbience with multiple samples and conditions
DropletUtils
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
jma1991
▴ 70
1
vote
1
reply
664
views
Input format for `combinations` in `hashedDrops`
DropletUtils
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
mikhael.manurung
▴ 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
Aaron Lun
★ 28k • written 3.0 years ago by
rohitsatyam102
▴ 20
35 results • Page
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Comment: deseq2 results
by
sajadahmad41454
• 0
thank you for your response, should i remove or discard that sample? since the red outlier on left represents one of healthy samples.
Comment: deseq2 results
by
swbarnes2
★ 1.4k
It looks like the PCA plot of a real RNASeq experiment. The red outlier on the left might be the mathematical reason why you have few vali…
Comment: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Dylan.Sheerin
• 0
Thank you very much, Gordon. I'll give voomLmFit a go!
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
by
Gordon Smyth
50k
Including subjectID in the design matrix always accounts for unbalanced sampling and patient variation but subjects with incomplete records…
Comment: Log-cpm values from limma
by
Gordon Smyth
50k
No, it does not mean that. `voom()` uses the design matrix with the W covariates, to compute precision weights but not to adjust the log-cp…
Votes
Comment: deseq2 results
Comment: deseq2 results
Answer: Multi-factorial, longitudinal disease progression analysis with unbalanced patie
Answer: Extremely small p-values using Limma for proteomic data
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