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Isoform
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2.1k
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Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
2.0 years ago • updated 23 months ago
priyanka.m
• 0
1
vote
5
replies
1.2k
views
Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
isoformswitchanalyzer
isoform
differential isoform usage
written 5.4 years ago by
A
▴ 40
0
votes
5
replies
1.3k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 3.7 years ago by
Gordon Smyth
50k • written 3.7 years ago by
Ina Hoeschele
▴ 620
1
vote
4
replies
1.1k
views
gene Isoforms quantification using RNA-seq data
gene
isoform
quantification
rna-seq
updated 4.6 years ago by
swbarnes2
★ 1.3k • written 4.6 years ago by
angel.campos
• 0
1
vote
4
replies
1.2k
views
Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer
Isoform
limma
IsoformSwitchAnalyzeR
updated 4.5 years ago by
k.vitting.seerup
▴ 120 • written 4.5 years ago by
asmita
• 0
0
votes
4
replies
1.0k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 3.8 years ago by
Gordon Smyth
50k • written 3.8 years ago by
Ina Hoeschele
▴ 620
0
votes
2
replies
559
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio
isoform
written 16 months ago by
lhaiyan3
• 0
0
votes
0
replies
1.3k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform
RNA-seq
hisat2
stringtie
ballgown
3.5 years ago
ra711
• 0
0
votes
0
replies
363
views
IsoformSwitchAnalyzer
Isoform
IsoformSwitchAnalyzeR
11 months ago
Craig
• 0
0
votes
0
replies
933
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
6.5 years ago
ilyco
• 0
10 results • Page
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Comment: DESeq filtering specific to contrasts
by
Carlin95
• 0
But wouldn't this result in a different gene set for each analysis stratification? How can you then compare if maybe gene x comes up in Tim…
Comment: Reading huge bismark coverage files using bbseq::read.bismark
by
jacques.imbert
• 0
Hello, Using nThread = 1L fixed the issue. Thank you for your time and help.
Comment: Error in champ.load(): The following specified files do not exist
by
Basti
▴ 760
The error stems from the Basename column, please see solution here : https://support.bioconductor.org/p/p132482/
Comment: FilterByExpr low counts with small sample size
by
Gordon Smyth
50k
As always, it helps to see code. Are you running `voom` or `voomLmFit`? Did you run `normLibSizes()` in edgeR prior to `voom`? Are you star…
Comment: Batch correction and repeated measures
by
Gordon Smyth
50k
In your code, it was clear that `expr.mat` was a matrix rather than a DGEList, so it has to be a count matrix. If you have a DGEList object…
Votes
Comment: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: Reading huge bismark coverage files using bbseq::read.bismark
Answer: How many of my genes from my gene list are in each KEGG pathway?
Comment: Light difference when using coef vs omit a group when compare 3 groups.
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