Bioconductor 10X

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951

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scrn 10x scRNAseq emptyDrops DropletUtils

4 months ago Peter Hickey ▴ 760

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1.7k

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labels PBMC SingleCellMultiModal 10X

updated 8 months ago by ATpoint ★ 5.0k • written 8 months ago by javier.ruizramirez • 0

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1.1k

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CellRanger emptyDrops scRNAseq 10X

21 months ago rocanja ▴ 60

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1.5k

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SingleCell emptyDrops 10X

updated 2.6 years ago by Peter Hickey ▴ 760 • written 2.6 years ago by sandra.garces.19 • 0

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1.2k

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RNAseq 10X

2.7 years ago wt215 • 0

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4.2k

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DropletUtils emptyDrops scRNA scRNAseq 10x

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

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1.6k

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DropletUtils emptyDrops 10x

updated 4.9 years ago by Aaron Lun ★ 29k • written 4.9 years ago by Peter Hickey ▴ 760

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2.2k

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deseq2 zinbwave 10X scRNA-seq Differential expression

updated 5.4 years ago by Michael Love 43k • written 5.4 years ago by vincent.croset ▴ 20

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3.8k

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10x scrna-seq

updated 6.6 years ago by Aaron Lun ★ 29k • written 6.6 years ago by jma1991 ▴ 70

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9.4k

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single-cell 10X Cell calling DropletUtils cellranger

updated 6.8 years ago by Aaron Lun ★ 29k • written 6.8 years ago by xingxd16 ▴ 20

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Answer: NUPOP usage by shepherl 4.2k

You should read the documentation in the package especially the package vignette https://bioconductor.org/packages/release/bioc/html/NuPoP.…

Comment: How can I correctly use phyloseq with Docker? by fnfgame • 0

In a rocker image, this error usually means the Bioconductor install happened as root but the runtime library paths used by the shiny user …

Comment: DECIPHER DesignProbes unable to design FISH-probes by Erik Wright ▴ 150

Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?

Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment by Michael Love 43k

BTW, I tested with no issue on MacOS ARM on our previous github issue.

Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment by Michael Love 43k

The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…

Votes

C: DESeq2 Following RSEM

Upcoming Ensembl API and data access changes - new blog post available

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?

Answer: Large logFC but somewhat high FDR

Comment: upstream git branches of bioc-release

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