Bioconductor Cuffdiff

Showing : Cuffdiff • reset

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4.5k

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dexseq bitseq cuffdiff Differential exon usage isoforms

10.6 years ago • updated 10.5 years ago elle ▴ 10

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4.3k

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htseqtools deseq2 counts cuffdiff

9.8 years ago Jon Bråte ▴ 270

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4.2k

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RNA-seq / XLOC cuffdiff

updated 3.9 years ago by Lan • 0 • written 5.6 years ago by mg.mahabad1365 • 0

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2.6k

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SpliceR Cuffdiff

updated 10.3 years ago by deppt002 • 0 • written 10.5 years ago by mfahim • 0

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2.1k

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cummeRbund Script analysis RNAseq cuffdiff

updated 10.6 years ago by andrew.j.skelton73 ▴ 370 • written 10.6 years ago by mfahim • 0

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2.1k

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WGCNA cuffdiff

7.2 years ago sbbinfo90 • 0

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2.1k

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deseq2 cuffdiff

updated 10.6 years ago by Michael Love 43k • written 10.6 years ago by a.de-giorgio12 • 0

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1.9k

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GAGE Cuffdiff gene names

updated 10.0 years ago by Luo Weijun ★ 1.6k • written 10.0 years ago by user31888 ▴ 30

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1.8k

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deseq2 cuffdiff differential gene expression

10.4 years ago Assa Yeroslaviz ★ 1.5k

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1.7k

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cuffdiff sqlite

8.1 years ago handgabriel • 0

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1.7k

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kegg readcufflinks cuffdiff cuff

updated 8.1 years ago by thokall ▴ 160 • written 8.1 years ago by pierre.biojoux • 0

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674

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cummeRbund cufflink cuffdiff

updated 2.4 years ago by James W. MacDonald 68k • written 2.4 years ago by sumitra • 0

12 results • Page 1 of 1

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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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