Log In
Sign Up
about
faq
Ask a question
Latest
News
Jobs
Tutorials
Tags
Users
New Post
Latest
News
Jobs
Tutorials
Tags
Users
Log In
Sign Up
About
Limit
all time
today
this week
this month
this year
Unanswered
All posts
Sort
Update
Answers
Bookmarks
Creation
Replies
Rank
Views
Votes
Showing :
dropletUtils
•
reset
3
votes
8
replies
891
views
DropletUtils read10xcounts adds the 12 Cell Multiplexing Oligo tags as gene names
DropletUtils
droplet
written 5 months ago by
pcantalupo
▴ 10
3
votes
1
reply
666
views
read10xCounts for Cell Ranger 7 Output
DropletUtils
updated 5 months ago by
ATpoint
★ 4.0k • written 18 months ago by
Dario Strbenac
★ 1.5k
0
votes
3
replies
661
views
insufficient unique points for computing knee/inflection points
DropletUtils
SingleCellData
updated 8 months ago by
ATpoint
★ 4.0k • written 8 months ago by
p.vlachou-efstathiou
• 0
0
votes
8
replies
1.6k
views
DropletUtils::read10xCounts error
read10xCounts
DropletUtils
15 months ago
fdumetz
• 0
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
5
votes
1
reply
4.4k
views
Error with DropletUtils::EmptyDrops()
DropletUtils
EmptyDrops
simpleSingleCell
updated 20 months ago by
Stefano Mangiola
▴ 10 • written 4.7 years ago by
shbrief
▴ 20
0
votes
1
reply
961
views
Aberrant number of cells
CellBarcode
DropletUtils
emptyDrops()
Cellranger
scRNAseq
updated 24 months ago by
rohitsatyam102
▴ 20 • written 2.2 years ago by
gregoire.destreel
• 0
1
vote
1
reply
647
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
0
votes
1
reply
864
views
Using controlAmbience with multiple samples and conditions
DropletUtils
updated 2.3 years ago by
Aaron Lun
★ 28k • written 2.3 years ago by
jma1991
▴ 70
1
vote
6
replies
1.4k
views
DropletUtils::swappedDrops segfault memory not mapped
DropletUtils
2.9 years ago
wesselyf
• 0
2
votes
1
reply
1.0k
views
barcodeRanks unusual warning "In smooth.spline(x[new.keep], y[new.keep], df = df, ...)"
DropletUtils
updated 2.9 years ago by
Aaron Lun
★ 28k • written 2.9 years ago by
rohitsatyam102
▴ 20
3
votes
2
replies
952
views
Should we apply DropletUtils on control case separately or on a common sce object.
DropletUtils
3.0 years ago
rohitsatyam102
▴ 20
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
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
Aaron Lun
★ 28k • written 3.3 years ago by
Peter Hickey
▴ 740
1
vote
3
replies
1.8k
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
1
reply
772
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
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
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 4.1 years ago by
Aaron Lun
★ 28k • written 4.1 years ago by
gil.stelzer
• 0
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
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
0
votes
1
reply
828
views
emptyDrops result is full NAs
scran
dropletUtils
scater
scRNA-Seq
4.9 years ago
hamza_karakurt
▴ 50
1
vote
3
replies
1.7k
views
Troubles with barcodeRanks()
DropletUtils
SingleCellExperiement
DelayedArray
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Steve Pederson
▴ 170
0
votes
2
replies
1.0k
views
Scalability of emptyDrops() running times
dropletutils
emptydrops
updated 4.9 years ago by
Aaron Lun
★ 28k • written 5.0 years ago by
rosano
• 0
1
vote
4
replies
976
views
Is there a limitation to the number of cells swappedDrops can handle?
swappedDrops
DropletUtils
5.0 years ago
joseph.joonsang
• 0
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
1
vote
2
replies
908
views
In which order should you detect empty droplets / remove barcode swapping using DropletUtils?
dropletutils
updated 5.0 years ago by
s1437643
▴ 20 • written 5.0 years ago by
jma1991
▴ 70
1
vote
2
replies
1.2k
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
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
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
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
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 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
7
votes
12
replies
7.0k
views
How to identify real cells in 10X RNA-seq ?
single-cell
10X
Cell calling
DropletUtils
cellranger
updated 5.1 years ago by
Aaron Lun
★ 28k • written 5.1 years ago by
xingxd16
▴ 20
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
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
7
votes
2
replies
2.3k
views
Recommendations for combining multiple 10x runs into one SingleCellExperiment
singlecellexperiment
dropletutils
simplesinglecell
updated 5.5 years ago by
Aaron Lun
★ 28k • written 5.5 years ago by
Peter Hickey
▴ 740
2
votes
4
replies
1.3k
views
Error when reading data with DropletUtils::read10xCounts
DropletUtils
updated 5.9 years ago by
Aaron Lun
★ 28k • written 5.9 years ago by
fabrost
• 0
35 results • Page
1 of 1
Recent ...
Replies
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
camp
▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Comment: Deseq2. decontXcounts not integers. Useful alternative?
by
ATpoint
★ 4.0k
I do not know this decontamination tool you use but generally: If these counts are basically "corrected" raw counts in the sense that they'…
Answer: Improving the design matrices vignette in RNAseq123
by
Gordon Smyth
50k
Thanks to Shian Su, we have confirmed that the problem in the design matrices vignette html is caused by a bug in knitr 1.44 (to do with sp…
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! I'll review my code from top to bottom.
Comment: Math expression in shapeCustom legend in EnhancedVolcano
by
James W. MacDonald
65k
So basically you are using HTML markup to set your subscripts and whatnot, and then `element_markdown` does the rest.
Votes
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
Answer: Cross-species analysis - how to compute the mid parent value?
Awards
• All
Scholar
to
James W. MacDonald
65k
Supporter
to
JKim
• 0
Popular Question
to
Gordon Smyth
50k
Popular Question
to
Chris
• 0
Supporter
to
Jonathan
▴ 10
Locations
• All
Germany,
just now
Pakistan,
just now
Ireland,
just now
UPF, Barcelona, Spain,
4 minutes ago
Pakistan,
22 minutes ago
Traffic: 933 users visited in the last hour
Content
Search
Users
Tags
Badges
Help
About
FAQ
Access
RSS
API
Stats
Use of this site constitutes acceptance of our
User Agreement and Privacy Policy
.
Powered by the
version 2.3.6