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gage package
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1
vote
2
replies
1.4k
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Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
7.7 years ago
joanito.liberti
• 0
2
votes
4
replies
1.7k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 6.7 years ago by
Gordon Smyth
50k • written 6.7 years ago by
sup230
▴ 30
0
votes
2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.2 years ago by
Helen
• 0 • written 6.2 years ago by
tarun2
• 0
5
votes
7
replies
2.8k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 6.0 years ago by
James W. MacDonald
65k • written 6.0 years ago by
Miskey, Csaba
▴ 20
1
vote
2
replies
1.1k
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
5.8 years ago
atakanekiz
▴ 30
0
votes
2
replies
1.6k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 7.5 years ago by
Luo Weijun
★ 1.6k • written 7.6 years ago by
Michael
• 0
0
votes
0
replies
899
views
GAGE for non model organism
gage package
gage
5.8 years ago
melkile26
• 0
0
votes
1
reply
936
views
Question on Gage
gage package
path.ids
RNA-Seq
7.8 years ago
rl1385
• 0
1
vote
0
replies
1.5k
views
DESeq2 - GAGE workflow
gage package
deseq2
6.8 years ago
sup230
▴ 30
0
votes
0
replies
913
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
7.8 years ago
smt8n
• 0
10 results • Page
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Comment: Why does GSEA on edgeR results for randomized samples give highly significant p-
by
gene_bioconductor
▴ 10
Thanks for your thoughtful and detailed comment, Gordon
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package)
by
Poonam
• 0
I looked into the genomic distributions. Please see the screenshot attatched ![ distrubution for female loci, boot1 and boot2][1] how do …
Answer: How to save the DEXSeq results
by
Michael Love
41k
If you look at the output here: https://bioconductor.org/packages/release/bioc/vignettes/DEXSeq/inst/doc/DEXSeq.html#4_Testing_for_differe…
Answer: Method to find pathways different between 2 groups
by
Robert Castelo
★ 3.3k
Hi, regarding how could you combine the result from each tool, one option is using a so-called "ensembl method", for instance, the package …
Answer: Couldn't connect to server while using "pathways"
by
James W. MacDonald
65k
As ATpoint already noted, you should proceed from the assumption that your audience knows nothing about what you are doing, and provide eno…
Votes
Answer: Method to find pathways different between 2 groups
Answer: Method to find pathways different between 2 groups
Answer: Why does GSEA on edgeR results for randomized samples give highly significant p-
Answer: Method to find pathways different between 2 groups
Comment: Trying to use enrichGO
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