Bioconductor 10X

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873

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scrn 10x scRNAseq emptyDrops DropletUtils

12 weeks ago • updated 11 weeks ago Peter Hickey ▴ 760

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1.6k

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labels PBMC SingleCellMultiModal 10X

updated 6 months ago by ATpoint ★ 5.0k • written 6 months ago by javier.ruizramirez • 0

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1.0k

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CellRanger emptyDrops scRNAseq 10X

19 months ago rocanja ▴ 60

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1.5k

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SingleCell emptyDrops 10X

updated 2.5 years ago by Peter Hickey ▴ 760 • written 2.5 years ago by sandra.garces.19 • 0

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1.2k

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RNAseq 10X

2.6 years ago wt215 • 0

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4.1k

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DropletUtils emptyDrops scRNA scRNAseq 10x

3.3 years ago • updated 3.2 years ago Peter Hickey ▴ 760

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1.5k

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DropletUtils emptyDrops 10x

updated 4.8 years ago by Aaron Lun ★ 29k • written 4.8 years ago by Peter Hickey ▴ 760

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2.1k

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 5.3 years ago by Michael Love 43k • written 5.3 years ago by vincent.croset ▴ 20

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3.7k

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10x scrna-seq

updated 6.5 years ago by Aaron Lun ★ 29k • written 6.5 years ago by jma1991 ▴ 70

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9.3k

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single-cell 10X Cell calling DropletUtils cellranger

updated 6.7 years ago by Aaron Lun ★ 29k • written 6.7 years ago by xingxd16 ▴ 20

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Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

I can reproduce this and have opened an issue on the code base https://github.com/Bioconductor/support.bioconductor.org/issues/112

Comment: "Watched Tags" are being erased rather than updated by shepherl 4.2k

we can investigate this issue. thank you for bringing it to our attention

Comment: deseq2 filter the low counts by Michael Love 43k

> But within each comparison (contrast), if I trace some DEGs back to the original salmon merged gene counts (or even to normalised counts)…

Comment: deseq2 filter the low counts by empty_mt • 0

Thank you for you suggestion to look at the pre-filtering section in the DESeq2 vignettes - am I missing something? I have 6 treatments, …

Comment: deseq2 filter the low counts by Michael Love 43k

Have you seen this part: https://bioconductor.org/packages/release/bioc/vignettes/DESeq2/inst/doc/DESeq2.html#pre-filtering

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Bioconductor 3.22 Released!

Comment: "Watched Tags" are being erased rather than updated

Comment: deseq2 filter the low counts

Answer: DESeq2 interactions

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