Bioconductor Isoforms

Showing : Isoforms • reset

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1.2k

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isoforms DESeq2

3.7 years ago arfranco ▴ 130

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3.2k

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RATs RNA-Seq Isoforms DTU expression

updated 6.4 years ago by fruce_ki ▴ 20 • written 6.4 years ago by UserAnonyme • 0

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isoforms diffrential expression noncoding rna TSIS isoformswitchanalyzeR

7.6 years ago rbenel ▴ 50

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1.3k

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dexseq differential isoform usage isoforms summarizeoverlaps granges

7.7 years ago A ▴ 60

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1.9k

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cummerbund heatmap isoforms transcript_id

8.7 years ago domenico.somma • 0

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4.5k

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dexseq bitseq cuffdiff Differential exon usage isoforms

10.5 years ago • updated 10.4 years ago elle ▴ 10

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3.1k

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edgeR ruvseq rnaseq isoforms

10.6 years ago • updated 10.5 years ago sergio.espeso-gil • 0

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1.8k

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DEXSeq transcripts isoforms

updated 10.6 years ago by Alejandro Reyes ★ 1.9k • written 10.6 years ago by peter_venhuizen • 0

8 results • Page 1 of 1

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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 …

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/

Votes

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