Showing : Isoforms • reset
5
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3
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edgeR: annotation and isoform analysis alternatives
edgeR ruvseq rnaseq isoforms
10.7 years ago • updated 10.6 years ago sergio.espeso-gil • 0
5
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18
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4.7k
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Incongruencies between DEXSeq and BitSeq/Cuffdiff
dexseq bitseq cuffdiff Differential exon usage isoforms
10.7 years ago • updated 10.6 years ago elle ▴ 10
2
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2
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1.3k
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Confounding DE results with DESeq2
isoforms DESeq2
3.8 years ago arfranco ▴ 130
1
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2
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1.8k
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DEXSeq transcripts per condition
DEXSeq transcripts isoforms
updated 10.7 years ago by ★ 1.9k • written 10.7 years ago by • 0
1
vote
9
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3.3k
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Difference between gene-level test and transcript-level test with RATs (Relative Abundance of Transcrits)
RATs RNA-Seq Isoforms DTU expression
updated 6.5 years ago by ▴ 20 • written 6.5 years ago by • 0
0
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3
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2.2k
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Downstream analysis for Salmon output: IsoformSwitchAnalyzeR or TSIS?
isoforms diffrential expression noncoding rna TSIS isoformswitchanalyzeR
7.7 years ago rbenel ▴ 50
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cummeRbund heatmap for specific isoforms (not genes)
cummerbund heatmap isoforms transcript_id
8.8 years ago domenico.somma • 0
0
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0
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1.4k
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Metadata sheet for DEXSeq analysis
dexseq differential isoform usage isoforms summarizeoverlaps granges
7.8 years ago A ▴ 60
8 results • Page 1 of 1
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Answer: When to use edgeR or limma by Gordon Smyth 53k
The short answer is that we generally prefer edgeR for applications with lots of small counts and limma for complex designs with random eff…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
I updated the above answer today.
Answer: When to use edgeR or limma by James W. MacDonald 68k
I would use edgeR's quasi-likelihood model for any analysis with a smaller number of observations (like 3 vs 3 or similar), but if you have…
Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
The short answer is that limpa reads standard feature-level intensities from Spectronaut or other quantifications tools. limpa is designed …
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Votes
A: deseq2 - paired samples in 2 sequencing types with very different library sizes
Comment: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
Answer: Question about the filterByExpr function inputs in edgeR
A: DESeq2: What is the unit of DESeq2 normalized read count (VST)? Is it tag per mi
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