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gageData
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Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.0 years ago
OST
• 0
6
votes
5
replies
1.5k
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KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.1 years ago by
Luo Weijun
★ 1.6k • written 3.1 years ago by
MOHAMMAD
• 0
0
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0
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627
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Setting threshold with gage for gene set analysis
gage
gageData
3.1 years ago
jd348
• 0
1
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2
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1.1k
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Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.3 years ago by
Emilia
▴ 30
4 results • Page
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Comment: The difference when using Limma compare between 3 conditions vs 2 conditions
by
Robert Castelo
★ 3.2k
Hi, your `c2` object storing all the gene sets is probably a `list` object, where element names are the names of the pathways given by MSig…
Comment: Differential peaks that were not identified in diffbind were identified in diseq
by
lonn
• 0
I tried the default normalization and got similar results as above. Perhaps I need to try identifying the difference peak without using dif…
Answer: Cannabis and KEGGgraph
by
deeenes
▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches
by
Gordon Smyth
50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param
by
russ.bainer
▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Votes
Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
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Robert Castelo
★ 3.2k
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James W. MacDonald
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shepherl
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Gordon Smyth
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