Showing : 10x • reset
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emptyDrops new default alpha = Inf giving far fewer non-empty droplets than under old default of alpha = NULL
scrn 10x scRNAseq emptyDrops DropletUtils
5 months ago Peter Hickey ▴ 760
1
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1
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1.7k
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Origin of the labels for the SingleCellMultiModal dataset
labels PBMC SingleCellMultiModal 10X
updated 9 months ago by ★ 5.0k • written 9 months ago by • 0
0
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2
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1.2k
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Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
22 months ago rocanja ▴ 60
0
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1
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1.6k
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Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 2.7 years ago by ▴ 760 • written 2.7 years ago by • 0
0
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2
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1.3k
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Compare and filter three BAM files
RNAseq 10X
2.8 years ago wt215 • 0
4
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5
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4.6k
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`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.5 years ago • updated 3.4 years ago Peter Hickey ▴ 760
1
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1
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1.6k
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Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils emptyDrops 10x
updated 5.0 years ago by ★ 29k • written 5.0 years ago by ▴ 760
5
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3
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2.3k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 5.5 years ago by 43k • written 5.5 years ago by ▴ 20
4
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2
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3.9k
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When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 70
7
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12
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9.8k
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How to identify real cells in 10X RNA-seq ?
single-cell 10X Cell calling DropletUtils cellranger
updated 6.9 years ago by ★ 29k • written 6.9 years ago by ▴ 20
10 results • Page 1 of 1
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Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Yes, Gender is more a nuisance factor in our experiment, and our primary interest is to compare groups. I will just use filter…
Comment: Joining different datasets and analyzing using the group-specific condition effe by jason.chai • 0
Thank you very much. I had read that and wondered if I used the recommendation in DESeq vignette, I would lose the pairing between groups? …
Comment: Questions about bacon QC and correction on EWAS results by sup0903 • 0
This is qq plot and histogram generated before bacon correction ![enter image description here][1] ![enter image description here][2] …
Votes
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
Answer: Clarification on counting in Rsubread (featureCounts)
Comment: Clarification on counting in Rsubread (featureCounts)
C: ControlGenes/ housekeeping genes Deseq2
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