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GAGE package
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1.0k
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GAGE for non model organism
gage package
gage
6.3 years ago
melkile26
• 0
1
vote
2
replies
1.4k
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
6.4 years ago
atakanekiz
▴ 30
5
votes
7
replies
3.0k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 6.5 years ago by
James W. MacDonald
67k • written 6.5 years ago by
Miskey, Csaba
▴ 20
0
votes
2
replies
4.0k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.7 years ago by
Helen
• 0 • written 6.8 years ago by
tarun2
• 0
2
votes
4
replies
2.1k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 7.3 years ago by
Gordon Smyth
51k • written 7.3 years ago by
sup230
▴ 30
1
vote
0
replies
1.6k
views
DESeq2 - GAGE workflow
gage package
deseq2
7.3 years ago
sup230
▴ 30
0
votes
2
replies
1.8k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 8.1 years ago by
Luo Weijun
★ 1.6k • written 8.1 years ago by
Michael
• 0
1
vote
2
replies
1.6k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
8.3 years ago
joanito.liberti
• 0
0
votes
1
reply
1.1k
views
Question on Gage
gage package
path.ids
RNA-Seq
8.3 years ago
rl1385
• 0
0
votes
0
replies
1.0k
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
8.4 years ago
smt8n
• 0
10 results • Page
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Replies
Answer: Deseq2 res Function
by
Michael Love
43k
> Does this mean the young and KO groups were numerators and denominators in the analysis, respectively? Read over the vignette and work…
Answer: ANOVA like approach of edgeR
by
Gordon Smyth
51k
You need to clarify whether interactions are present for the two factors in your study. In the two factors do not interact, then the code y…
Answer: Create Illmina bead summary data
by
Gordon Smyth
51k
GenomeStudio produces IDAT files that you can read using the `read.idat` function in limma. That is the recommended way to read GenomeStudi…
Comment: Help with RSEM counts: do I transpose matrix?
by
NB
• 0
OK thank you.
Comment: Help with RSEM counts: do I transpose matrix?
by
James W. MacDonald
67k
You can ask here, but please read the `DESeq2` vignette first, which should answer most questions.
Votes
Answer: Deseq2 res Function
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification
Answer: ANOVA like approach of edgeR
Answer: ANOVA like approach of edgeR
Comment: ANOVA like approach of edgeR
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