Bioconductor 10X

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198

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CellRanger emptyDrops scRNAseq 10X

5 weeks ago rocanja ▴ 60

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657

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SingleCell emptyDrops 10X

updated 11 months ago by Peter Hickey ▴ 740 • written 11 months ago by sandra.garces.19 • 0

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619

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RNAseq 10X

13 months ago wt215 • 0

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2.3k

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DropletUtils emptyDrops scRNA scRNAseq 10x

21 months ago • updated 20 months ago Peter Hickey ▴ 740

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1.0k

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DropletUtils emptyDrops 10x

updated 3.3 years ago by Aaron Lun ★ 28k • written 3.3 years ago by Peter Hickey ▴ 740

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1.3k

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 3.8 years ago by Michael Love 41k • written 3.8 years ago by vincent.croset ▴ 20

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2.3k

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10x scrna-seq

updated 5.0 years ago by Aaron Lun ★ 28k • written 5.0 years ago by jma1991 ▴ 70

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7.0k

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single-cell 10X Cell calling DropletUtils cellranger

updated 5.1 years ago by Aaron Lun ★ 28k • written 5.1 years ago by xingxd16 ▴ 20

8 results • Page 1 of 1

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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…

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…

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?

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Popular Question to James W. MacDonald 65k

Scholar to Michael Love 41k

Supporter to JKim • 0