Bioconductor GTEx

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DESeq2 recount GTEx TCGA recount3

updated 2.6 years ago by ATpoint ★ 5.0k • written 2.6 years ago by David ▴ 20

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recount3 TCGA GTEx DESeq2

3.5 years ago David ▴ 20

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DESeq2 GTEx

4.8 years ago Bine ▴ 50

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recount gtex

updated 7.1 years ago by Leonardo Collado Torres ★ 1.1k • written 7.1 years ago by abe • 0

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limma voom gtex

7.7 years ago mico • 0

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rnaseq deseq2 gtex

updated 8.0 years ago by Michael Love 43k • written 8.0 years ago by vikram • 0

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public data TCGA GTEx Tutorial

8.3 years ago shepherl 4.2k

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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…

Answer: Question about DESeq2 Design for Paired Treatment Study by ATpoint ★ 5.0k

It's a paired analysis so you don't need any patient-specific covariates such as age and sex. What you call batch effect might just be the …

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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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Commentator to sina.nassiri ▴ 130