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News:
Announcing the GBCC2025 Logo Design Contest!
Conference
Community
Galaxy
GBCC2025
Bioconductor
6 months ago
Maria Doyle
▴ 100
0
votes
2
replies
1.3k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 2.2 years ago by
swbarnes2
★ 1.4k • written 2.2 years ago by
mbxdn1
• 0
0
votes
1
reply
1.2k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 3.2 years ago by
Michael Love
43k • written 3.2 years ago by
István
• 0
0
votes
3
replies
2.0k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 2.9 years ago by
Kevin Blighe
★ 4.0k • written 4.7 years ago by
lakshmi9c
• 0
0
votes
1
reply
701
views
deseq2 for enrichments between different subcellular fractions?
deseq2
galaxy
updated 5.0 years ago by
Michael Love
43k • written 5.0 years ago by
mikelirastor
• 0
1
vote
3
replies
1.6k
views
Running DESeq2 inside local Galaxy instance
deseq2
galaxy
8.0 years ago
gkuffel
▴ 10
0
votes
2
replies
1.6k
views
Data analysis in R
bioconductor
next-generation sequencing
galaxy
updated 8.3 years ago by
Lucas Schiffer
▴ 240 • written 8.3 years ago by
efraim.culfa
• 0
0
votes
4
replies
4.6k
views
Using DESeq2 inside Galaxy
rnaseq
galaxy
deseq2
updated 9.1 years ago by
Michael Love
43k • written 9.2 years ago by
Marcelo Pereira
▴ 70
0
votes
2
replies
1.4k
views
Inverting order of groups when using DESeq2
DESeq2
Galaxy
updated 9.1 years ago by
Michael Love
43k • written 9.1 years ago by
Marcelo Pereira
▴ 70
9 results • Page
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Comment: Bioconductor 3.20 Release Schedule
by
randyprice13102000
• 0
This offers much info https://bioconductor.org/checkResults/release/bioc-LATEST/
Comment: Filtering after DESeq
by
ATpoint
★ 4.8k
The problem is that your prefilter is not group-aware so the behaviour of seeing these sorts of outliers is expected. This is why I always …
Comment: GSEA preranked analysis downstream of DEseq2
by
ATpoint
★ 4.8k
All due respect, this is what people do since pvalues exist, so this paper is not a reference, not is this a special score that merits a na…
Comment: Check removeBatchEffect effectiveness
by
ATpoint
★ 4.8k
> insert size, mean GC, etc... This is not a classical "batch" in the common sense, at least I've never seen this to be corrected for expl…
Answer: Check removeBatchEffect effectiveness
by
Gordon Smyth
52k
Your call to removeBatchEffect() is not correct because that function does not have an argument called `batch3`, meaning that the batch fac…
Votes
Answer: DiffBind; Error: No sites have activity greater than filter value
DiffBind; Error: No sites have activity greater than filter value
remove X and Y chromosome genes in RNA-seq data using DESeq2 pipeline
How to remove X & Y chromosome genes from RNAseq data
Is it advisable to remove X and Y chromosome genes in mouse bulk RNA-seq data at the level of the count matrix?
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