Showing : junctionseq • reset
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JunctionSeq producing strangely large effect sizes for certain exon counting bins
junctionseq splicing RNAseq DEXSeq
written 6.1 years ago by ▴ 10
2
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Question: Error when running QoRTs for JunctionSeq
DEXSeq JunctionSeq RNAseq QoRTs
4.9 years ago • updated 4.8 years ago n.tear ▴ 20
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JunctionSeq/DEXSeq: Dispersion plot looks strange (but is fine in DESeq2)
deseq2 junctionseq dexseq estimatedispersions rnaseq
updated 9.1 years ago by ★ 13k • written 9.1 years ago by • 0
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JunctionSeq Can't produce Summary Plots
JunctionSeq
8.7 years ago rachelrodgers12 • 0
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Setting relevel with the JunctionSeq package
junctionseq relevel reference
8.9 years ago Assa Yeroslaviz ★ 1.5k
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JunctionSeq pairwise contrast with a multi-level treatment
junctionseq design and contrast matrix
9.2 years ago stuart • 0
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JunctionSeq on multiple conditions
junctionseq qorts multiple factor design relevel
8.9 years ago Assa Yeroslaviz ★ 1.5k
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1.1k
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Problems running JunctionSeq
junctionseq
9.2 years ago jbono ▴ 10
8 results • Page 1 of 1
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Answer: limpa-blank normalization and Spectronaut's PTM stoichiometry by Gordon Smyth 53k
limpa reads standard feature-level output from Spectronaut. You do not need to make any changes to the output before reading it into limpa.…
Comment: Question about the filterByExpr function inputs in edgeR by mohammedtoufiq91 ▴ 10
@gordonsmyth Noted, thank you very much.
Comment: Question about the filterByExpr function inputs in edgeR by Gordon Smyth 53k
Regarding edgeR v4 filtering, I didn't mention anything about a minimum count of 10 but rather said "a positive count". So a minimalistic f…
Comment: limpa-blank normalization and Spectronaut's PTM stoichiometry by JKim • 0
Hi Emily, He left some comments regarding normalization. Here is the relevant quote: > The EList object produced by dpcQuant(), containi…
Comment: Joining different datasets and analyzing using the group-specific condition effe by James W. MacDonald 68k
Yes, making a group factor simplifies things, and you will need a new column for disease subject to avoid having a design that is not full …
Votes
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
Answer: Clarification on counting in Rsubread (featureCounts)
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