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Isoform
•
reset
6
votes
10
replies
3.4k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 11 months ago by
ATpoint
★ 5.0k • written 11 months ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
734
views
IsoformSwitchAnalyzer
Isoform
IsoformSwitchAnalyzeR
2.5 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 3.0 years ago by
lhaiyan3
• 0
0
votes
5
replies
3.3k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
3.6 years ago • updated 3.5 years ago
priyanka.m
• 0
0
votes
0
replies
2.0k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform
RNA-seq
hisat2
stringtie
ballgown
5.1 years ago
ra711
• 0
0
votes
5
replies
2.0k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 5.3 years ago by
Gordon Smyth
53k • written 5.3 years ago by
Ina Hoeschele
▴ 620
0
votes
4
replies
1.7k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 5.3 years ago by
Gordon Smyth
53k • written 5.3 years ago by
Ina Hoeschele
▴ 620
1
vote
4
replies
1.9k
views
Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer
Isoform
limma
IsoformSwitchAnalyzeR
updated 6.1 years ago by
k.vitting.seerup
▴ 120 • written 6.1 years ago by
asmita
• 0
1
vote
4
replies
1.6k
views
gene Isoforms quantification using RNA-seq data
gene
isoform
quantification
rna-seq
updated 6.2 years ago by
swbarnes2
★ 1.4k • written 6.2 years ago by
angel.campos
• 0
1
vote
5
replies
1.9k
views
Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
isoformswitchanalyzer
isoform
differential isoform usage
written 6.9 years ago by
A
▴ 60
0
votes
0
replies
1.3k
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
8.0 years ago
ilyco
• 0
11 results • Page
1 of 1
Recent ...
Replies
Comment: Getting a large intercept with DESeq2
by
Michael Love
43k
Thanks James -- Denise you can check the "note on factor levels" in the vignette. And I'd recommend `plotCounts()` for looking at individu…
Comment: Getting a large intercept with DESeq2
by
James W. MacDonald
68k
As a trivial example, consider this: ``` > model.matrix(~Treatment, data.frame(Treatment = factor(rep(1:3, each = 4)))) (Intercept) Tre…
Answer: Getting a large intercept with DESeq2
by
James W. MacDonald
68k
The default parameterization in R is a treatment-contrasts parameterization that sets one of your groups as the baseline. So the intercept …
Answer: Must I do pseudobulk analysis on Cell Surface Protein Labeling data of Single C
by
ATpoint
★ 5.0k
There is no "MUST", but pseudobulk aggregation is beneficial to a) enable use of tested and robust methods such as limma (though it could u…
Answer: Post translational modifications and phosphoproteomics in limpa?
by
Gordon Smyth
53k
Yes, we use limpa for PTMs ourselves. I assume your data is preprocessed so that each row corresponds to a PTM. You replace dpcQuant() with…
Votes
Answer: What R/Bioconductor tools would you recommend for the analysis of sncRNA, specif
Using edgeR or DESeq2 to analyze allele-specific expression?
Answer: DESeq2 design for haplotype MPRA
Answer: Failure to download resources (MeSHDb) from AnnotationHub
Answer: Failure to download resources (MeSHDb) from AnnotationHub
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