Bioconductor GenomicAlignments

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1.1k

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VariantAnnotation Annotation GenomicRanges VariantAnnotation GenomicAlignments Annotation

11.3 years ago Valerie Obenchain ★ 6.8k

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2.5k

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VariantTools BiocParallel GenomicAlignments VariantTools BiocParallel GenomicAlignments

updated 11.5 years ago by Martin Morgan 25k • written 11.5 years ago by Guest User ★ 13k

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1.9k

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RNASeq Cancer convert Rsamtools GenomicAlignments RNASeq Cancer convert Rsamtools

updated 11.5 years ago by Stefano Calza ▴ 90 • written 11.5 years ago by Valerie Obenchain ★ 6.8k

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1.7k

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RNASeq GenomicAlignments RNASeq GenomicAlignments

updated 11.6 years ago by Valerie Obenchain ★ 6.8k • written 11.6 years ago by Stefano Calza ▴ 90

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2.2k

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Alignment Cancer convert GenomicAlignments Alignment Cancer convert GenomicAlignments

updated 11.7 years ago by Hervé Pagès 16k • written 11.7 years ago by Niu, Liang NIH/NIEHS [E] ▴ 50

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Coverage GenomicAlignments Coverage GenomicAlignments

11.8 years ago Hervé Pagès 16k

106 results • Page 3 of 3

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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 …

Comment: problem reading bam files into nucleR by efoss ▴ 10

I thought I might be able to track down a problematic line in the bam file by repeatedly splitting the bam file in and then running the co…

Answer: two questions about limma by Gordon Smyth 53k

Answered here: https://support.bioconductor.org/p/16318/

Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication? by Ahmed Salah • 0

Thank you very much! will take that into consideration

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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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