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DropletUtils
•
reset
0
votes
8
replies
640
views
DropletUtils::read10xCounts error
read10xCounts
DropletUtils
4 months ago
fdumetz
• 0
0
votes
0
replies
289
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
7 months ago
Dario Strbenac
★ 1.5k
4
votes
5
replies
1.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
10 months ago • updated 9 months ago
Peter Hickey
▴ 650
0
votes
1
reply
527
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 13 months ago by
rohitsatyam102
▴ 20 • written 16 months ago by
gregoire.destreel
• 0
1
vote
1
reply
422
views
Input format for `combinations` in `hashedDrops`
DropletUtils
updated 16 months ago by
Aaron Lun
★ 28k • written 16 months ago by
mikhael.manurung
▴ 270
0
votes
1
reply
511
views
Using controlAmbience with multiple samples and conditions
DropletUtils
updated 17 months ago by
Aaron Lun
★ 28k • written 17 months ago by
jma1991
▴ 70
1
vote
6
replies
841
views
DropletUtils::swappedDrops segfault memory not mapped
DropletUtils
2.0 years ago
wesselyf
• 0
2
votes
1
reply
551
views
barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df, ...)"
DropletUtils
updated 2.0 years ago by
Aaron Lun
★ 28k • written 2.0 years ago by
rohitsatyam102
▴ 20
3
votes
2
replies
608
views
Should we apply DropletUtils on control case separately or on a common sce object.
DropletUtils
2.1 years ago
rohitsatyam102
▴ 20
2
votes
4
replies
805
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
Peter Hickey
▴ 650
1
vote
1
reply
639
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
Peter Hickey
▴ 650
1
vote
3
replies
1.3k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 2.4 years ago by
Aaron Lun
★ 28k • written 2.4 years ago by
msn
• 0
0
votes
1
reply
525
views
DropletUtils::swappedDrops - Kallisto instead of CellRanger?
DropletUtils
updated 2.5 years ago by
Aaron Lun
★ 28k • written 2.5 years ago by
mhalache
• 0
4
votes
5
replies
1.4k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 2.6 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
C T
▴ 140
0
votes
7
replies
946
views
DropletUtils::swappedDrops more cells than using Read10x with filtered_feature_bc_matrix files
10x genomics
DropletUtils
single cell RNA seq
updated 3.2 years ago by
Aaron Lun
★ 28k • written 3.2 years ago by
gil.stelzer
• 0
0
votes
3
replies
820
views
Running DropletUtils::swappedDrops() on multiplexed samples from different libraries
swappeddrops
dropletutils
updated 3.6 years ago by
Aaron Lun
★ 28k • written 3.6 years ago by
rosano
• 0
0
votes
4
replies
657
views
DropletUtils' emptyDrops() fails with non-integer counts
DropletUtils
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
jmanning
• 0
5
votes
1
reply
3.6k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 9 months ago by
stefano.mangiola
▴ 10 • written 3.8 years ago by
shbrief
▴ 20
0
votes
1
reply
533
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.0 years ago
hamza_karakurt
▴ 50
1
vote
3
replies
1.2k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.0 years ago by
Steve Pederson
▴ 170
0
votes
2
replies
694
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 4.0 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
rosano
• 0
1
vote
4
replies
636
views
Is there a limitation to the number of cells swappedDrops can handle?
swappedDrops
DropletUtils
4.1 years ago
joseph.joonsang
• 0
2
votes
5
replies
821
views
Recommendations for running DropletUtils::swappedDrops() on multiplexed samples from multiple libraries
dropletutils
swappeddrops
updated 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
rosano
• 0
1
vote
2
replies
573
views
In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
dropletutils
updated 4.1 years ago by
s1437643
▴ 10 • written 4.1 years ago by
jma1991
▴ 70
1
vote
2
replies
928
views
Segmentation Fault with development versions of R, Bioconductor, and DropletUtils when processing output of CellRanger 3.0.2
DropletUtils
Bioc-devel
4.2 years ago
Matthew Thornton
▴ 350
0
votes
4
replies
1.2k
views
Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into DropletUtils
DropletUtils
h5
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
Matthew Thornton
▴ 350
0
votes
1
reply
684
views
Can DropletUtils Package be used to identify cells for 10X VDJ data ?
DropletUtils
10X 5` TCR
single cells
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
xingxd16
▴ 20
2
votes
2
replies
752
views
What`s new features in DropletUtils version 1.3.10 comapred to version 1.2.2
DropletUtils
Bioconductor
singel cell
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
xingxd16
▴ 20
7
votes
12
replies
5.6k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 4.2 years ago by
Aaron Lun
★ 28k • written 4.2 years ago by
xingxd16
▴ 20
1
vote
5
replies
737
views
about DropletUtils and scRNA-seq
dropseq
dropletutils
droplet
updated 4.4 years ago by
Aaron Lun
★ 28k • written 4.4 years ago by
Bogdan
▴ 660
0
votes
2
replies
805
views
DropletUtils barcodeRanks bug (?)
dropletutils
updated 4.5 years ago by
Aaron Lun
★ 28k • written 4.5 years ago by
jmanning
• 0
7
votes
2
replies
1.7k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 4.6 years ago by
Aaron Lun
★ 28k • written 4.6 years ago by
Peter Hickey
▴ 650
2
votes
4
replies
909
views
Error when reading data with DropletUtils::read10xCounts
DropletUtils
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
fabrost
• 0
33 results • Page
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Answer: DESeq2 + analysis question for design with uneven time point design
by
Michael Love
40k
I'd recommend reaching out to a local statistician or someone familiar with linear models in R. Unfortunately, I have to reserve my time on…
Answer: Genes with highest differential expression have very low read counts for most ge
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Michael Love
40k
Have you use `lfcShrink`? Or `results` with `lfcThreshold`? Either of these are recommended for prioritizing DE genes.
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47k
> equivqalent in limma would be like a gene by gene specificic design matrix where no BL time point would exist but a continuous variable t…
Comment: Extract Limma Adjusted Values for Plotting
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ATpoint
★ 2.9k
Yes, with normalized counts on log2 scale.
Comment: Adjusting for baseline when having longitudinal data, mixed model and no treat
by
Anna
▴ 20
A no I never referred to transcriptomic data when I was talking about "standard procedure" I was referring to the way we analyze longitudin…
Votes
A: Ranges from a fasta file
Answer: NA transcript values in my Txdb
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Answer: Use with_go along with other filters in getBM function
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