Showing : 10x • reset
0
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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
3 months ago • updated 12 weeks ago Peter Hickey ▴ 760
1
vote
1
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1.6k
views
Origin of the labels for the SingleCellMultiModal dataset
labels PBMC SingleCellMultiModal 10X
updated 7 months ago by ★ 5.0k • written 7 months ago by • 0
0
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2
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1.0k
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
20 months ago rocanja ▴ 60
0
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1
reply
1.5k
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 2.5 years ago by ▴ 760 • written 2.5 years ago by • 0
0
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2
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1.2k
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Compare and filter three BAM files
RNAseq 10X
2.6 years ago wt215 • 0
4
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5
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4.1k
views
`emptyDrops()` calling 'too many' non-empty droplets
DropletUtils emptyDrops scRNA scRNAseq 10x
3.3 years ago • updated 3.2 years ago Peter Hickey ▴ 760
1
vote
1
reply
1.5k
views
Number of non-empty drops returned by emptyDrops() depends on value of test.ambience
DropletUtils emptyDrops 10x
updated 4.8 years ago by ★ 29k • written 4.8 years ago by ▴ 760
5
votes
3
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2.1k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 5.3 years ago by 43k • written 5.3 years ago by ▴ 20
4
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2
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3.7k
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When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 6.5 years ago by ★ 29k • written 6.5 years ago by ▴ 70
7
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12
replies
9.3k
views
How to identify real cells in 10X RNA-seq ?
single-cell 10X Cell calling DropletUtils cellranger
updated 6.7 years ago by ★ 29k • written 6.7 years ago by ▴ 20
10 results • Page 1 of 1
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Answer: Add additional maintainer for MOFA2 by shepherl 4.2k
These requests are best on the bioc-devel @ r-project.org or a request to maintainer @ bioconductor.org -- We would ideally need the curre…
Answer: After running samtools, the featureCounts command crashed. by Kevin Blighe ★ 4.0k
Hi Rui Tang, The "buffer overflow detected" error in featureCounts usually stems from a corrupted or malformed GTF file, often due to tr…
Answer: Problem with the TMB plot by Kevin Blighe ★ 4.0k
Hi, The linear TMB plot with no clustering suggests your variant calls may lack sample-specific discrimination, likely due to filtering ap…
Answer: gene Set with high AUC score but no cells assigned to cell type by Kevin Blighe ★ 4.0k
Hi, You have correctly identified the issue: AUCell's automatic threshold selection is conservative by design, aiming for specificity to…
Answer: featureCounts -L: high unassigned:mapq fraction by Kevin Blighe ★ 4.0k
Hi Katarzyna, The discrepancy arises because your samtools stats were restricted to genic regions only, where alignments are typically o…
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Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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