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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
504
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
1 of 1
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Comment: gds in GEOmetadb 2023-06-26 version is empty
by
Frederico Moraes Ferreira
▴ 100
Try axel -n 20 https://gbnci.cancer.gov/geo/GEOmetadb.sqlite.gz
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
James W. MacDonald
66k
The default for `enrichGO` is to subset to those with a p-value<0.05. You don't adjust that default argument, so you shouldn't have any GO …
Answer: In a 3 group DEG analysis with three batches, can I use 1 group in all three bat
by
Michael Love
42k
You can compare A and C thanks to the sharing of samples from B across 1, 2 and 3.
Comment: Most enriched pathway is not expressed when modifying universe parameter
by
adripel
• 0
In the enrichGO results we have significant and non-significant enriched terms that are displayed. So why would an enriched term (significa…
Answer: Design formula, numeric contrast, and lfcshrink in deseq2
by
Michael Love
42k
For questions about how to construct the correct contrasts correspond to particular hypotheses, I recommend consulting with a local statist…
Votes
Comment: Most enriched pathway is not expressed when modifying universe parameter
Time-course, comparison of two groups
Answer: Behaviour of featureCounts when quantifying multi-mapping reads
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`
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