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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 15 months ago by
swbarnes2
★ 1.4k • written 15 months ago by
mbxdn1
• 0
0
votes
1
reply
882
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 2.3 years ago by
Michael Love
42k • written 2.3 years ago by
István
• 0
0
votes
3
replies
1.5k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 24 months ago by
Kevin Blighe
★ 3.9k • written 3.9 years ago by
lakshmi9c
• 0
0
votes
1
reply
503
views
deseq2 for enrichments between different subcellular fractions?
deseq2
galaxy
updated 4.2 years ago by
Michael Love
42k • written 4.2 years ago by
mikelirastor
• 0
1
vote
3
replies
1.4k
views
Running DESeq2 inside local Galaxy instance
deseq2
galaxy
7.2 years ago
gkuffel
▴ 10
0
votes
2
replies
1.3k
views
Data analysis in R
bioconductor
next-generation sequencing
galaxy
updated 7.5 years ago by
Lucas Schiffer
▴ 240 • written 7.5 years ago by
efraim.culfa
• 0
0
votes
4
replies
4.1k
views
Using DESeq2 inside Galaxy
rnaseq
galaxy
deseq2
updated 8.2 years ago by
Michael Love
42k • written 8.3 years ago by
Marcelo Pereira
▴ 70
0
votes
2
replies
1.2k
views
Inverting order of groups when using DESeq2
DESeq2
Galaxy
updated 8.2 years ago by
Michael Love
42k • written 8.2 years ago by
Marcelo Pereira
▴ 70
8 results • Page
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Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
Hi James, thank you for your answer. I understand how the pvalue might be significant or not depending on the universe. But I still don't …
Comment: GESA with certain gene list returns no result with human genom, but many result
by
sawa
• 0
Thank you so much! I did not know the rule that human genes are written in upper case and mouse in first letter capitalized format. When I …
Comment: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
by
isaac.vock
• 0
Thank you for looking into this and for your explanation! As a follow-up, would it be possible in future releases of featureCounts to pro…
Comment: error loading collectTRI regulon
by
silvaesilva.da
• 0
Fantastic. Thank you very much. Everything has been sorted out
Answer: DESeq2 returns results for group with just one replicate
by
James W. MacDonald
66k
There is no problem having only one replicate per group, so long as you have replicates for other groups. The degrees of freedom are based …
Votes
Answer: GESA with certain gene list returns no result with human genom, but many result
Answer: Odd behavior of Rsubread::featureCounts when setting `nonOverlap = 0`
Answer: DESeq2 returns results for group with just one replicate
Answer: DESeq2 returns results for group with just one replicate
Comment: error loading collectTRI regulon
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