Bioconductor Snps

Showing : snps • reset

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3.5k

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snps VCF

updated 3.6 years ago by Arafat • 0 • written 8.8 years ago by rkdonthu ▴ 10

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934

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hierClust R SNPs clustering

updated 3.7 years ago by James W. MacDonald 68k • written 3.7 years ago by sekhwal • 0

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1.4k

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SNPs

6.7 years ago pltbiotech_tkarthi • 0

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1.6k

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snps vcf venn diagram ggplot2

6.9 years ago mictadlo ▴ 10

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1.7k

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bioconductor molecular biology snps

updated 7.0 years ago by James W. MacDonald 68k • written 7.0 years ago by jebreen20 • 0

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3.3k

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motifbreakR vcf snps motif analysis

updated 7.5 years ago by Valerie Obenchain ★ 6.8k • written 7.5 years ago by svlachavas ▴ 840

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2.0k

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variantannotation SNPs txdb.hsapiens.ucsc.hg19.knowngene ucsc

updated 8.5 years ago by Valerie Obenchain ★ 6.8k • written 8.5 years ago by Lna • 0

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1.8k

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hsapiens snps indels

updated 10.0 years ago by Hervé Pagès 16k • written 10.0 years ago by kredens • 0

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2.0k

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Biostrings SNPs alignment

updated 10.4 years ago by Hervé Pagès 16k • written 10.4 years ago by ben.ward ▴ 30

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2.3k

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gviz ideogram snps

updated 10.9 years ago by florian.hahne@novartis.com ★ 1.6k • written 10.9 years ago by vnyirongo • 0

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2.7k

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overlap snps granges iranges

updated 11.2 years ago by Michael Lawrence ★ 11k • written 11.2 years ago by anastasiya-terskih ▴ 10

11 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