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News:
Announcing the GBCC2025 Logo Design Contest!
Conference
Community
Galaxy
GBCC2025
Bioconductor
13 months ago
Maria Doyle
▴ 110
0
votes
2
replies
1.5k
views
DESeq2 analysis on Galaxy. PCA plot shows my replicates do not cluster and large intragroup variability
DESeq2
Galaxy
pca
updated 2.8 years ago by
swbarnes2
★ 1.4k • written 2.8 years ago by
mbxdn1
• 0
0
votes
1
reply
1.4k
views
Controlling for sex variance in Galaxy DESeq2
DESeq2
RNASeq
Galaxy
updated 3.8 years ago by
Michael Love
43k • written 3.8 years ago by
István
• 0
0
votes
3
replies
2.3k
views
StringTie output as Ballgown input
ballgown
StringTie
galaxy
rnaseq
updated 3.5 years ago by
Kevin Blighe
★ 4.0k • written 5.4 years ago by
lakshmi9c
• 0
0
votes
1
reply
813
views
deseq2 for enrichments between different subcellular fractions?
deseq2
galaxy
updated 5.6 years ago by
Michael Love
43k • written 5.6 years ago by
mikelirastor
• 0
1
vote
3
replies
1.8k
views
Running DESeq2 inside local Galaxy instance
deseq2
galaxy
8.6 years ago
gkuffel
▴ 10
0
votes
2
replies
1.8k
views
Data analysis in R
bioconductor
next-generation sequencing
galaxy
updated 9.0 years ago by
Lucas Schiffer
▴ 240 • written 9.0 years ago by
efraim.culfa
• 0
0
votes
4
replies
4.9k
views
Using DESeq2 inside Galaxy
rnaseq
galaxy
deseq2
updated 9.7 years ago by
Michael Love
43k • written 9.8 years ago by
Marcelo Pereira
▴ 70
0
votes
2
replies
1.6k
views
Inverting order of groups when using DESeq2
DESeq2
Galaxy
updated 9.7 years ago by
Michael Love
43k • written 9.7 years ago by
Marcelo Pereira
▴ 70
9 results • Page
1 of 1
Recent ...
Replies
Comment: DECIPHER DesignProbes unable to design FISH-probes
by
Erik Wright
▴ 150
Are the sequences aligned (i.e., the same width) before running `TileSeqs()`?
Comment: BiocParallel (and DESeq2) - wrong args for environment subassignment
by
Michael Love
43k
BTW, I tested with no issue on MacOS ARM on our previous github issue.
Answer: DESeq(dds, parallel=TRUE) wrong args for environment subassignment
by
Michael Love
43k
The DESeq2 error makes sense, as we've talked about, given that the simple `bplapply` isn't working in your setup. Maybe give the traceb…
Answer: PTM analysis in LIMPA
by
Gordon Smyth
53k
For PTM analysis, the usual quantification command dpcQuant() is replaced by dpcImpute(). Otherwise the limpa pipeline is the same as for a…
Answer: problem reading bam files into nucleR
by
James W. MacDonald
68k
The first step is to update to the current versions of R/Bioconductor and try again. It's possible that you have run into a bug that's alre…
Votes
C: DESeq2 Following RSEM
Upcoming Ensembl API and data access changes - new blog post available
Comment: Highly similar RNA-seq samples in PCA - pooling or technical duplication?
Answer: Large logFC but somewhat high FDR
Comment: upstream git branches of bioc-release
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