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dropletutils
•
reset
3
votes
8
replies
1.3k
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 11 months ago by
pcantalupo
▴ 10
3
votes
1
reply
845
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
updated 12 months ago by
ATpoint
★ 4.5k • written 2.1 years ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
1000
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 15 months ago by
ATpoint
★ 4.5k • written 15 months ago by
p.vlachou-efstathiou
• 0
0
votes
8
replies
2.0k
views
DropletUtils::read10xCounts error
read10xCounts
DropletUtils
22 months ago
fdumetz
• 0
4
votes
5
replies
3.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils
emptyDrops
scRNA
scRNAseq
10x
2.3 years ago • updated 2.2 years ago
Peter Hickey
▴ 740
0
votes
1
reply
1.2k
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 2.5 years ago by
rohitsatyam102
▴ 20 • written 2.8 years ago by
gregoire.destreel
• 0
1
vote
1
reply
817
views
Input format for `combinations` in `hashedDrops`
DropletUtils
updated 2.8 years ago by
Aaron Lun
★ 28k • written 2.8 years ago by
mikhael.manurung
▴ 280
0
votes
1
reply
1.1k
views
Using controlAmbience with multiple samples and conditions
DropletUtils
updated 2.8 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
jma1991
▴ 70
1
vote
6
replies
1.6k
views
DropletUtils::swappedDrops segfault memory not mapped
DropletUtils
3.5 years ago • updated 3.4 years ago
wesselyf
• 0
2
votes
1
reply
1.2k
views
barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df, ...)"
DropletUtils
updated 3.5 years ago by
Aaron Lun
★ 28k • written 3.5 years ago by
rohitsatyam102
▴ 20
3
votes
2
replies
1.2k
views
Should we apply DropletUtils on control case separately or on a common sce object.
DropletUtils
3.5 years ago
rohitsatyam102
▴ 20
2
votes
4
replies
1.4k
views
Does hashedDrops support 'imbalanced' combinations of HTOs?
DropletUtils
scRNAseq
updated 3.7 years ago by
Aaron Lun
★ 28k • written 3.7 years ago by
Peter Hickey
▴ 740
1
vote
1
reply
1.2k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils
emptyDrops
10x
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
Peter Hickey
▴ 740
1
vote
3
replies
2.1k
views
10X FeatureBarcode producing too many "cells"
SingleCellExperiment
DropletUtils
SingleCellData
updated 3.8 years ago by
Aaron Lun
★ 28k • written 3.8 years ago by
msn
▴ 10
0
votes
1
reply
927
views
DropletUtils::swappedDrops - Kallisto instead of CellRanger?
DropletUtils
updated 3.9 years ago by
Aaron Lun
★ 28k • written 3.9 years ago by
mhalache
• 0
4
votes
5
replies
2.2k
views
emptyDrops identified less non-empty cells with lower total UMI counts?
DropletUtils
scRNA-seq
emptyDrops
simplesinglecell
cell calling
updated 4.0 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
C T
▴ 140
0
votes
7
replies
1.8k
views
DropletUtils::swappedDrops more cells than using Read10x with filtered_feature_bc_matrix files
10x genomics
DropletUtils
single cell RNA seq
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
gil.stelzer
• 0
0
votes
3
replies
1.4k
views
Running DropletUtils::swappedDrops() on multiplexed samples from different libraries
swappeddrops
dropletutils
updated 5.0 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
rosano
• 0
0
votes
4
replies
1.2k
views
DropletUtils' emptyDrops() fails with non-integer counts
DropletUtils
updated 5.2 years ago by
Aaron Lun
★ 28k • written 5.2 years ago by
jmanning
• 0
5
votes
1
reply
4.9k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 2.2 years ago by
Stefano Mangiola
▴ 20 • written 5.3 years ago by
shbrief
▴ 20
0
votes
1
reply
994
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
5.4 years ago
hamza_karakurt
▴ 60
1
vote
3
replies
1.8k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 5.4 years ago by
Aaron Lun
★ 28k • written 5.4 years ago by
Steve Pederson
▴ 170
0
votes
2
replies
1.3k
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
rosano
• 0
1
vote
4
replies
1.2k
views
Is there a limitation to the number of cells swappedDrops can handle?
swappedDrops
DropletUtils
5.5 years ago
joseph.joonsang
• 0
2
votes
5
replies
1.4k
views
Recommendations for running DropletUtils::swappedDrops() on multiplexed samples from multiple libraries
dropletutils
swappeddrops
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
rosano
• 0
1
vote
2
replies
1.1k
views
In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
dropletutils
updated 5.6 years ago by
s1437643
▴ 20 • written 5.6 years ago by
jma1991
▴ 70
1
vote
2
replies
1.5k
views
Segmentation Fault with development versions of R, Bioconductor, and DropletUtils when processing output of CellRanger 3.0.2
DropletUtils
Bioc-devel
5.6 years ago
Matthew Thornton
▴ 380
0
votes
4
replies
2.1k
views
Error importing molecule_info.h5 file generated by Cell Ranger 3.0.2 into DropletUtils
DropletUtils
h5
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
Matthew Thornton
▴ 380
0
votes
1
reply
1.2k
views
Can DropletUtils Package be used to identify cells for 10X VDJ data ?
DropletUtils
10X 5` TCR
single cells
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
xingxd16
▴ 20
2
votes
2
replies
1.2k
views
What`s new features in DropletUtils version 1.3.10 comapred to version 1.2.2
DropletUtils
Bioconductor
singel cell
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
xingxd16
▴ 20
7
votes
12
replies
7.8k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.7 years ago by
Aaron Lun
★ 28k • written 5.7 years ago by
xingxd16
▴ 20
1
vote
5
replies
1.4k
views
about DropletUtils and scRNA-seq
dropseq
dropletutils
droplet
updated 5.8 years ago by
Aaron Lun
★ 28k • written 5.8 years ago by
Bogdan
▴ 670
0
votes
2
replies
1.2k
views
DropletUtils barcodeRanks bug (?)
dropletutils
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
jmanning
• 0
7
votes
2
replies
2.8k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Peter Hickey
▴ 740
2
votes
4
replies
1.5k
views
Error when reading data with DropletUtils::read10xCounts
DropletUtils
updated 6.4 years ago by
Aaron Lun
★ 28k • written 6.4 years ago by
fabrost
• 0
35 results • Page
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Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Thank you!
Comment: Combining RNAseq and microarray data using edgeR/limma-voom
by
Adam Marstrand
• 0
Hi Gordon, Thanks for the answer! This makes a lot of sense. Your suggested pipeline (separate processing of datasets -> gene set analyses…
Comment: How many of my genes from my gene list are in each KEGG pathway?
by
josephasmith1310
• 0
> You can compare the number in the column setSize versus the number of > genes in core_enrichment. The former corresponds to the number of…
Comment: EuroBioC2024 abstract submission is open!
by
Esperan
• 0
Great information about the EuroBioC2024 conference! https://openreview.net/group?id=bioconductor.org/EuroBioC/2024/Conferences [slope](htt…
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
by
Gordon Smyth
51k
I agree with James, although I tend to combine analyses using geneset tests rather than by meta analysis tools like GeneMeta. > My questio…
Votes
Answer: Combining RNAseq and microarray data using edgeR/limma-voom
Answer: How do I merge a list of GRanges?
A: p.adjust BH generates duplicate values
Answer: Adjusted p-values become NA when sub-setting samples
Comment: Suggestion for FGSEA and GSEA creation for C57BL/6J Mice
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