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GAGE package
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1.1k
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GAGE for non model organism
gage package
gage
6.6 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
6.6 years ago
atakanekiz
▴ 30
5
votes
7
replies
3.1k
views
Gage package; go.gset() function error: argument "go_id" is missing
gage package
error
updated 6.8 years ago by
James W. MacDonald
68k • written 6.8 years ago by
Miskey, Csaba
▴ 20
0
votes
2
replies
4.1k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 3.0 years ago by
Helen
• 0 • written 7.0 years ago by
tarun2
• 0
2
votes
4
replies
2.2k
views
Can't find gene list for KEGG genesets
kegg
geneset
genelist
gage package
updated 7.5 years ago by
Gordon Smyth
52k • written 7.5 years ago by
sup230
▴ 30
1
vote
0
replies
1.7k
views
DESeq2 - GAGE workflow
gage package
deseq2
7.6 years ago
sup230
▴ 30
0
votes
2
replies
1.9k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage
gage package
updated 8.3 years ago by
Luo Weijun
★ 1.6k • written 8.4 years ago by
Michael
• 0
1
vote
2
replies
1.7k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
8.5 years ago
joanito.liberti
• 0
0
votes
1
reply
1.1k
views
Question on Gage
gage package
path.ids
RNA-Seq
8.6 years ago
rl1385
• 0
0
votes
0
replies
1.1k
views
GAGE package statistical tests
t-test
GAGE package
Kolmogorov-Smirnov test
Gene-Set enrichment
8.6 years ago
smt8n
• 0
10 results • Page
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Answer: EuroBioC2023 abstract submission is open!
by
cirwin009
• 0
Submit here https://openreview.net/group?id=bioconductor.org/EuroBioC/2023/ [Block Blast][1] This article offers a thorough and in-depth…
Comment: How to formulate 2 factor nested design in DESeq2
by
Mariane
• 0
Hi JK Kim, I'm having a problem similar to the one you reported. Could you please tell me how you solved this problem? Thanks
Comment: batch effect removal for agilent microarray data
by
gaye.yilmaz
• 0
Thank you
Answer: Pathview visualisation not including positive log2 fold changes
by
James W. MacDonald
68k
Without providing a self-contained example, nobody can tell you if/where you went wrong. Since you get a KEGG pathway with some of the gene…
Comment: Differential variance analysis - can i use deseq2
by
Marwan
• 0
Thanks Michael for your answer, i didnt mean to use Deseq2 directly for the variance testing, but more like asking if using the (VST) data…
Votes
Answer: Differential expression of protein coding ENSGs (Ensembl IDs) | When to biomaRt?
Suggesting changing the "reply-to" field to the mailing list address.
Answer: UniProt.ws query for single UniRef90 ID takes several minutes
A: How to extract DESeq2 results for an interaction design
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K?
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