Showing : 10X • reset
7
votes
12
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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 ★ 28k • written 5.1 years ago by ▴ 20
5
votes
3
replies
1.3k
views
Latent factors for differential expression
deseq2 zinbwave 10X scRNA-seq Differential expression
updated 3.8 years ago by 41k • written 3.8 years ago by ▴ 20
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
4
votes
2
replies
2.3k
views
When to combine samples in the pre-processing of 10x scRNA-seq data?
10x scrna-seq
updated 5.0 years ago by ★ 28k • written 5.0 years ago by ▴ 70
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 ★ 28k • written 3.3 years ago by ▴ 740
0
votes
2
replies
198
views
Non-empty droplets versus good quality cells
CellRanger emptyDrops scRNAseq 10X
5 weeks ago rocanja ▴ 60
0
votes
2
replies
619
views
Compare and filter three BAM files
RNAseq 10X
13 months ago wt215 • 0
0
votes
1
reply
657
views
Choosing the right lower limit for emptyDrops
SingleCell emptyDrops 10X
updated 11 months ago by ▴ 740 • written 11 months ago by • 0
8 results • Page 1 of 1
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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
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…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
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
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