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simplesinglecell
•
reset
4
votes
5
replies
2.0k
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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
6
replies
1.2k
views
Feature selection across batches in simpleSingleCell when spike-ins are not available.
simpleSingleCell
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
1
vote
1
reply
669
views
Feature selection across batches in simpleSingleCell "Correcting batch effects" vignette
simpleSingleCell
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
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
1
vote
5
replies
1.6k
views
Preprocessing in scran::doubletCells
scran
simpleSingleCell
updated 4.7 years ago by
Aaron Lun
★ 28k • written 4.7 years ago by
Angelos Armen
• 0
4
votes
4
replies
2.8k
views
using limma and edgeR for differential expression of Drop-seq/10xGenomics scRNA-seq data
limma
edgeR
simplesingleCell
scran
scater
updated 4.8 years ago by
Aaron Lun
★ 28k • written 4.8 years ago by
Bogdan
▴ 670
4
votes
2
replies
1.6k
views
single cell data: adding random effects for subject with multilevel experiment design
SingleCellExperiment
scran
limma
simpleSingleCell
updated 4.9 years ago by
Aaron Lun
★ 28k • written 4.9 years ago by
Matt Mulé
• 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 4.9 years ago by
Steve Pederson
▴ 170
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
0
votes
1
reply
849
views
Unusual graph for Identifying HVGs from the normalized log-expression
workflows
simplesinglecell
updated 5.6 years ago by
Aaron Lun
★ 28k • written 5.6 years ago by
es.azadian
• 0
0
votes
1
reply
939
views
The explanation of plotExplanatoryVariables plot
simplesinglecell
updated 6.1 years ago by
Aaron Lun
★ 28k • written 6.1 years ago by
Xingyu
• 0
1
vote
2
replies
1.8k
views
SingleCellExperiment object cannot be used by Scater package?
scater
singlecellexperiment
simplesinglecell
updated 6.2 years ago by
Aaron Lun
★ 28k • written 6.2 years ago by
Xingyu
• 0
3
votes
2
replies
3.1k
views
Sparse matrices in Bioconductor objects for single-cell analyses
scater
simpleSingleCell
workflows
updated 6.8 years ago by
Aaron Lun
★ 28k • written 6.8 years ago by
sandmann.t
▴ 70
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Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Comment: DESeq2 output used for PCA plot on R studio
by
Aaliya
• 0
I had taken this code from internet, but after reading about it and I did on my own, I would be making a post to ask for the suggestions if…
Comment: featureCounts reports an error:"featureCounts: input-files.c:2890: SAM_pairer_ge
by
shuwangxinze1996
• 0
Hello, I used 48 cpus and 320G of memory to run this program. My bam files size are 7-9G, wonder how much CPU and memory is enough?
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
This comment helps.
Comment: DESeq2 output used for PCA plot on R studio
by
Kevin Blighe
★ 3.9k
I am not sure how your comment helps here?
Votes
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
Answer: How to retrieve gene ontology GO class from gene list?
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