Bioconductor Girafe

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2.8k

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BSgenome hexbin BSgenome IRanges genomeIntervals GenomicRanges girafe Rsamtools HiTC HiTC

updated 12.0 years ago by Dan Tenenbaum ★ 8.2k • written 12.0 years ago by Wim Kreinen ▴ 100

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Annotation girafe Annotation girafe

updated 13.4 years ago by Joern Toedling ▴ 50 • written 13.4 years ago by karlerhard@berkeley.edu ▴ 60

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1.7k

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girafe girafe

updated 13.7 years ago by Sean Davis 21k • written 13.7 years ago by chunjiang he ▴ 80

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1.1k

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girafe girafe

updated 13.9 years ago by Joern Toedling ▴ 10 • written 13.9 years ago by karlerhard@berkeley.edu ▴ 60

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1000

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Annotation girafe Annotation girafe

updated 14.0 years ago by Hervé Pagès 16k • written 14.0 years ago by karlerhard@berkeley.edu ▴ 60

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1.8k

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edgeR girafe edgeR girafe

updated 14.0 years ago by Hervé Pagès 16k • written 14.0 years ago by karlerhard@berkeley.edu ▴ 60

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1.5k

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edgeR girafe edgeR girafe

updated 14.0 years ago by Chris Fields ▴ 90 • written 14.0 years ago by karlerhard@berkeley.edu ▴ 60

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1.0k

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Alignment annotate girafe Alignment annotate girafe

updated 14.8 years ago by Joern Toedling ▴ 450 • written 14.8 years ago by Andreia Fonseca ▴ 810

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1.5k

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Annotation annotate biomaRt IRanges girafe Annotation annotate biomaRt IRanges girafe

updated 14.8 years ago by Joern Toedling ▴ 450 • written 14.8 years ago by Andreia Fonseca ▴ 810

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1.2k

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girafe girafe

updated 14.8 years ago by Steve Lianoglou ★ 13k • written 14.8 years ago by Andreia Fonseca ▴ 810

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Comment: Improving performance of edgeR and limma while adjusting for multiple confounder by ATpoint ★ 4.8k

If 2 minutes is inacceptable to you then you can still fall back to limma-trend which should give a dramatic speedup and finish in seconds.…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Mike Smith ★ 6.6k

Great, thanks for the update from Ensembl. So the most relevant part of 'Location: Scaffold HG1277_PATCH: 137,021-141,806 forward strand' …

Answer: Improving performance of edgeR and limma while adjusting for multiple confounder by Gordon Smyth 52k

We recommend that you use voomLmFit() instead of voom+lmFit. We are pretty proud of the speed of glmQLFit and voom, and we hadn't expected…

Answer: Merging EPICV1 and V2 betas by James W. MacDonald 68k

It appears that [SeSAMe][1] has functions meant to do that sort of thing. [1]: https://bioconductor.org/packages/release/bioc/vignet…

Comment: getBM from biomaRt inconsistencies found with .gtf files across multiple species by Benjamin ▴ 20

I have received a response from Ensembl regarding the items I have listed above. I wanted to post it here and will continue to post update…

Votes

Looking for equivalent EPIC chip v1 vs. v2 annotation variables

Properly constructing a hypergeometric test

A: Is logFC a log2 fold change or some other base in scran::findMarkers

Comment: Error in retrieving clinical data

What is the cheapest day to fly on American Airlines? {Ask_Expert}

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