Bioconductor 10x

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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

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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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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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1.3k

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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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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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652

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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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615

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RNAseq 10X

13 months ago wt215 • 0

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195

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CellRanger emptyDrops scRNAseq 10X

5 weeks ago rocanja ▴ 60

8 results • Page 1 of 1

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Answer: DESEQ2 IHW and Apelgm method for Shrinkage (adding s values to FDR) by Michael Love 41k

> I got many p values that had "1.000000e+00" and padj "1" and stat of "0" when I added the Log threshold of LFC >1 and LFC < -1...is this …

Comment: Trying to use enrichGO by fernanda.backsouza ▴ 10

With all my love, thank you Guido, GOxploreR beeing a big ally for me. I don't know how to be grateful right now.

Comment: DESeq2 output used for PCA plot on R studio by swbarnes2 ★ 1.3k

You didn't generate it with an experiment, you made it up: Your PCA doesn't look like a good RNASeq experiment, because it's not.

Answer: Opposite sign of LFC in count plots of DEGs (DESeq2) by swbarnes2 ★ 1.3k

Your contrast is comparing LGR5 to Homeostasis. The bottom 2 are fine, it's the top one that is wrong. Are you sure this step isn't misla…

Comment: get BM error by James W. MacDonald 65k

I believe you need NCBI Gene IDs for KEGG, in which case you may need to map. The three genes you have shown here don't map, and of those t…

Votes

C: when to apply quantile normalization with voom in limma/voom framework with RNA-

A: How to know if I should use voomWithQualityWeights() or not?

A: Weird results (ribosomal proteins / Y-linked genes) in limma/voom

Answer: Log-cpm values from limma

Awards • All

Teacher to Gordon Smyth 50k