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galaxy
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DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 14 months ago by
swbarnes2
★ 1.3k • written 14 months ago by
mbxdn1
• 0
0
votes
1
reply
849
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 2.2 years ago by
Michael Love
41k • written 2.2 years ago by
István
• 0
0
votes
3
replies
1.4k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 22 months ago by
Kevin Blighe
★ 3.9k • written 3.8 years ago by
lakshmi9c
• 0
0
votes
1
reply
487
views
deseq2 for enrichments between different subcellular fractions?
deseq2
galaxy
updated 4.0 years ago by
Michael Love
41k • written 4.0 years ago by
mikelirastor
• 0
1
vote
3
replies
1.4k
views
Running DESeq2 inside local Galaxy instance
deseq2
galaxy
7.0 years ago
gkuffel
▴ 10
0
votes
2
replies
1.3k
views
Data analysis in R
bioconductor
next-generation sequencing
galaxy
updated 7.4 years ago by
Lucas Schiffer
▴ 240 • written 7.4 years ago by
efraim.culfa
• 0
0
votes
4
replies
4.0k
views
Using DESeq2 inside Galaxy
rnaseq
galaxy
deseq2
updated 8.1 years ago by
Michael Love
41k • written 8.2 years ago by
Marcelo Pereira
▴ 70
0
votes
2
replies
1.1k
views
Inverting order of groups when using DESeq2
DESeq2
Galaxy
updated 8.1 years ago by
Michael Love
41k • written 8.1 years ago by
Marcelo Pereira
▴ 70
8 results • Page
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Comment: CombineArrays for EPIC and EPIC V2
by
Kim
• 0
Thank you Tim, this is a great help in getting me started!
Comment: Too many significant genes when integrating gtex and tcga
by
Michael Love
41k
Yes, this was one of the aspects we highlighted in the 2014 paper, and it's also in the workflow. Check these places first. Also take a st…
Answer: Too many significant genes when integrating gtex and tcga
by
James W. MacDonald
65k
See `?results`, in particular the lfcThreshold argument.
Comment: Once again a "Model matrix not full rank"
by
James W. MacDonald
65k
You already ran a temporal assay. Now you can compare each time point to the baseline. The interaction term is only applicable if you have…
Comment: Timecourse RNASeq analysis
by
Aurora
• 0
I managed to run ImpulseDE2 as I am interested in getting significant gene changes over time. Now I would like to run deseq as well and com…
Votes
Answer: CombineArrays for EPIC and EPIC V2
Answer: Too many significant genes when integrating gtex and tcga
Comment: Too many significant genes when integrating gtex and tcga
A: Print Differentially Expressed Exons From Dexseq Results
stuck on unimplemented type 'list' in 'EncodeElement'
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