Bioconductor Sushi

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sushi bed

7.2 years ago maltethodberg ▴ 180

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969

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sushi plotGenes

7.9 years ago portia.mcghan • 0

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sushi

9.2 years ago snamjoshi87 ▴ 40

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sushi plotBed data.frame

9.7 years ago waqasnayab • 0

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sushi plotBed

updated 9.7 years ago by dphansti ▴ 10 • written 9.9 years ago by Dimitris Polychronopoulos ▴ 80

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1.3k

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Sushi

updated 9.7 years ago by dphansti ▴ 10 • written 9.7 years ago by Till ▴ 30

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2.6k

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R sushi

updated 9.9 years ago by dphansti ▴ 10 • written 9.9 years ago by javier.mendoza • 0

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sushi

updated 10.3 years ago by Steve Lianoglou ★ 13k • written 10.3 years ago by Bogdan ▴ 670

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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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