Bioconductor Des

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279

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des DESeq2

written 3 months ago by fedor.bezrukov ▴ 10

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645

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DESeq2 des

updated 17 months ago by James W. MacDonald 68k • written 17 months ago by Atul K. • 0

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1.8k

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DESeq2 RUVSeq RUVseq BatchEffect DES

updated 19 months ago by James W. MacDonald 68k • written 19 months ago by Alexandre • 0

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632

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Des DESeq2

updated 20 months ago by hemantcnaik • 0 • written 20 months ago by Sahar • 0

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780

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DESeq2 DEs

21 months ago feather-W • 0

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903

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DESeq2 des

updated 3.0 years ago by Michael Love 43k • written 3.1 years ago by Devin • 0

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994

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DES DESIGN

updated 3.2 years ago by Michael Love 43k • written 3.2 years ago by mike • 0

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1.2k

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DESeq2 DES

updated 5.0 years ago by Michael Love 43k • written 5.0 years ago by heikki.sarin ▴ 10

8 results • Page 1 of 1

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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…

Answer: PTM analysis in LIMPA by Gordon Smyth 53k

For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…

Answer: problem reading bam files into nucleR by James W. MacDonald 68k

The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…

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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