Bioconductor Differential isoform usage

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DRIMSeq splicing differential isoform usage

updated 8.2 years ago by Gosia Nowicka ▴ 90 • written 8.2 years ago by kristoffer.vittingseerup ▴ 20

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isoformswitchanalyzer isoform differential isoform usage

written 6.3 years ago by A ▴ 60

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tximport differential isoform usage salmon tss rna-seq

7.8 years ago Steffen Heyne ▴ 10

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kallisto differential isoform usage isoform

7.4 years ago ilyco • 0

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dexseq differential isoform usage isoforms summarizeoverlaps granges

7.0 years ago A ▴ 60

5 results • Page 1 of 1

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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…

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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

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Answer: Merging annotation with differential expression output

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