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isoform
•
reset
6
votes
10
replies
3.0k
views
What type of counts data to import for performing Isoform analysis in edgeR
limma
isoform
edgeR
salmon
R
updated 5 months ago by
ATpoint
★ 4.8k • written 5 months ago by
mohammedtoufiq91
▴ 10
0
votes
0
replies
619
views
IsoformSwitchAnalyzer
Isoform
IsoformSwitchAnalyzeR
2.0 years ago
Craig
• 0
0
votes
2
replies
941
views
Does the knock down cause transcriptome-wide differences in isoform usage for Pac-Bio data?
pacbio
isoform
written 2.5 years ago by
lhaiyan3
• 0
0
votes
5
replies
3.0k
views
Can Differential Isoform expression analysis can be performed using DESeq2 package
RNASeqData
isoform
DESeq2
3.1 years ago • updated 3.0 years ago
priyanka.m
• 0
0
votes
0
replies
1.8k
views
HISAT2/StringTie/Ballgown for Novel Transcript Isoform Differential Expression
isoform
RNA-seq
hisat2
stringtie
ballgown
4.6 years ago
ra711
• 0
0
votes
5
replies
1.8k
views
isoform data, deep sequencing and voom
isoform
deep sequencing
voom
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
Ina Hoeschele
▴ 620
0
votes
4
replies
1.5k
views
mean-variance trend plots with isoform and gene-level data from tximport
tximport
isoform
voom
updated 4.8 years ago by
Gordon Smyth
52k • written 4.8 years ago by
Ina Hoeschele
▴ 620
1
vote
4
replies
1.7k
views
Identify recurrent isoform switches using IsoformSwitchAnalyzeR in multiple rectal tumor samples
cancer
Isoform
limma
IsoformSwitchAnalyzeR
updated 5.6 years ago by
k.vitting.seerup
▴ 120 • written 5.6 years ago by
asmita
• 0
1
vote
4
replies
1.5k
views
gene Isoforms quantification using RNA-seq data
gene
isoform
quantification
rna-seq
updated 5.7 years ago by
swbarnes2
★ 1.4k • written 5.7 years ago by
angel.campos
• 0
1
vote
5
replies
1.6k
views
Can DEXSeq ouput be used directly as an input for IsoformSwitchAnalyzeR
isoformswitchanalyzer
isoform
differential isoform usage
written 6.5 years ago by
A
▴ 60
0
votes
0
replies
1.2k
views
IsoformSwitchAnalyzeR error input
kallisto
differential isoform usage
isoform
7.6 years ago
ilyco
• 0
11 results • Page
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Replies
Answer: Limma suqeezeVar
by
Gordon Smyth
52k
I am not quite clear why you're not using the limma package directly, because it will compute all the variances and the df automatically fo…
Comment: Discrepancies in normalised count data vs unnormalised
by
swbarnes2
★ 1.4k
Well, that's going to make each sample normalize quite differently. So you should expect large difference between normalized and unnormali…
Comment: Can't install BioC packages (and manager) behind firewall
by
Marcel Ramos
700
Hi Delphine, Please make sure that your SSL certificates are up to date. Check with your system's administrator. Your browser may be usin…
Comment: Limma trend with limpa
by
Alejandro
• 0
Dear Gordon, Thank you very much!
Answer: DESeq2 from phyloseq error
by
asafpr
• 0
Apparently, I left this line: ```r setClassUnion("ExpData", c("matrix", "SummarizedExperiment")) ``` to patch the ExpData issue which was …
Votes
Deseq2 DE analysis of host-pathogen samples (model separately or jointly?)
Comment: Check removeBatchEffect effectiveness
Answer: Check removeBatchEffect effectiveness
A: what should I do with many zero counts from Salmon quantification
Comment: parameters of filterByExpr
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