Showing : Isoform • reset
6
votes
10
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3.6k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma isoform edgeR salmon R
updated 13 months ago by ★ 5.0k • written 13 months ago by ▴ 10
1
vote
5
replies
2.0k
views
Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
isoformswitchanalyzer isoform differential isoform usage
written 7.1 years ago by ▴ 60
1
vote
4
replies
1.7k
views
gene Isoforms quantification using RNA-seq data
gene isoform quantification rna-seq
updated 6.4 years ago by ★ 1.4k • written 6.4 years ago by • 0
1
vote
4
replies
2.0k
views
Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer Isoform limma IsoformSwitchAnalyzeR
updated 6.3 years ago by ▴ 120 • written 6.3 years ago by • 0
0
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5
replies
3.4k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData isoform DESeq2
3.7 years ago • updated 3.6 years ago priyanka.m • 0
0
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0
replies
781
views
IsoformSwitchAnalyzer
Isoform IsoformSwitchAnalyzeR
2.7 years ago Craig • 0
0
votes
2
replies
1.1k
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio isoform
written 3.1 years ago by • 0
0
votes
5
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2.1k
views
isoform data, deep sequencing and voom
isoform deep sequencing voom
updated 5.4 years ago by 53k • written 5.4 years ago by ▴ 620
0
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4
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1.8k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport isoform voom
updated 5.5 years ago by 53k • written 5.5 years ago by ▴ 620
0
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0
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1.3k
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IsoformSwitchAnalyzeR error input
kallisto differential isoform usage isoform
8.2 years ago ilyco • 0
0
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0
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2.0k
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HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform RNA-seq hisat2 stringtie ballgown
5.3 years ago ra711 • 0
11 results • Page 1 of 1
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Replies
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
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…
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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