Bioconductor Refseq

Showing : refseq • reset

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1.2k

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refseq Bioconductor conversion

5.0 years ago heiko_kin ▴ 60

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896

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RefSeq Chromosome Mutalyzer

5.7 years ago heiko_kin ▴ 60

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2.9k

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tximport Gene IDs txdb RefSeq Salmon

updated 5.9 years ago by Michael Love 43k • written 5.9 years ago by holmkn • 0

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3.5k

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edgeR ENEMBL RefSeq

updated 6.7 years ago by Gordon Smyth 53k • written 6.7 years ago by mzillur • 0

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3.2k

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genomicfeatures maketxdbfromucsc refseq

updated 9.4 years ago by Hervé Pagès 16k • written 9.4 years ago by Sebastien Vigneau ▴ 10

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4.6k

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ncbi refseq maketxdbfromgff fetchExtendedChromInfoFromUCSC genomeinfodb

updated 9.9 years ago by Hervé Pagès 16k • written 9.9 years ago by gokcen.eraslan ▴ 10

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3.6k

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promoter granges refseq ucsc organismdb

updated 10.0 years ago by Robert Castelo ★ 3.4k • written 10.0 years ago by efoss ▴ 10

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4.3k

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refseq annotationhub

updated 10.2 years ago by Martin Morgan 25k • written 10.2 years ago by dalloliogm ▴ 50

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2.1k

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customprodb dbsnp refseq varianttools

updated 10.4 years ago by xiaojing.wang ▴ 50 • written 10.4 years ago by kristenbeck527 • 0

9 results • Page 1 of 1

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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 …

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

Awards • All

Commentator to sina.nassiri ▴ 130