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Showing :
gage
•
reset
0
votes
13
replies
2.1k
views
Gage and setp argument
gsea
gage
8.0 years ago • updated 7.9 years ago
peter.chernek
• 0
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
20 months ago • updated 14 months ago
nute11a
▴ 10
0
votes
13
replies
5.8k
views
gage pathways enrichment analysis
gage
pathways
kegg
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.4 years ago by
francesca.defilippis
▴ 100
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
6.8 years ago • updated 6.7 years ago
Luo Weijun
★ 1.6k
0
votes
9
replies
3.1k
views
Urgent: Do GAGE applicable for non model species?
gage
updated 8.8 years ago by
amywingsze
• 0 • written 8.8 years ago by
jackipchiho
▴ 10
4
votes
7
replies
7.2k
views
Comparison between two different group's pathway analysis results
gage
DESeq2
pathway analysis
updated 4.7 years ago by
mikhael.manurung
▴ 270 • written 4.7 years ago by
tntntntntn
▴ 10
0
votes
7
replies
4.7k
views
Simple pathway enrichment analysis for gene lists
Microarray
Category
gage
KEGGREST
ROntoTools
Microarray
Category
gage
KEGGREST
ROntoTools
updated 10.6 years ago by
Paul Shannon
▴ 470 • written 10.6 years ago by
enricoferrero
▴ 660
0
votes
6
replies
3.5k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage
pathview
error
updated 7.8 years ago by
Luo Weijun
★ 1.6k • written 7.9 years ago by
marie.bordone
• 0
0
votes
6
replies
2.6k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage
gsea
rnaseq
updated 9.0 years ago by
Luo Weijun
★ 1.6k • written 9.0 years ago by
Tom
• 0
6
votes
5
replies
1.5k
views
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
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 2.8 years ago by
najib
• 0 • written 5.8 years ago by
bekah
▴ 40
4
votes
5
replies
1.7k
views
GAGE after tximport
gage
tximport
updated 6.5 years ago by
Luo Weijun
★ 1.6k • written 6.5 years ago by
Ed Siefker
▴ 230
0
votes
5
replies
2.3k
views
Rgraphviz installation issue
Rgraphviz
gage
Rgraphviz
gage
updated 10.3 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
km
▴ 100
2
votes
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps
GAGE
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 years ago by
user31888
▴ 30
0
votes
4
replies
2.0k
views
Error: Pathway analysis using Sleuth results
pathview
gage
rna-seq
R
sleuth
7.3 years ago
bioinf
▴ 10
0
votes
4
replies
1.9k
views
EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways
gsea
egsea
gage
updated 7.6 years ago by
Monther Alhamdoosh
▴ 40 • written 7.6 years ago by
yingchen
• 0
0
votes
4
replies
2.2k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage
pathview
8.6 years ago
martin.hoelzer
▴ 20
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 7.4 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
rubi
▴ 110
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO
gage
goseq
KEGG
updated 9.5 years ago by
Gordon Smyth
50k • written 9.6 years ago by
Merienne Nicolas
▴ 120
0
votes
4
replies
1.2k
views
kegg.gsets: unknown species
gage
4.6 years ago
mel.p
• 0
0
votes
4
replies
3.2k
views
Pathview for global and overview maps Re: using pathview about hsa01100
Pathways
graph
PROcess
SIM
gage
pathview
Pathways
graph
PROcess
SIM
gage
pathview
updated 10.7 years ago by
Ed
▴ 230 • written 10.7 years ago by
Luo Weijun
★ 1.6k
0
votes
3
replies
2.3k
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
Microarray
GO
Cancer
Breast
gage
Microarray
GO
Cancer
Breast
gage
updated 12.3 years ago by
Javerjung Sandhu
▴ 200 • written 12.3 years ago by
Valerie Obenchain
★ 6.8k
1
vote
3
replies
1.5k
views
DESeq2 rlog as input for GAGE
deseq2
gage
7.8 years ago
Tom
▴ 10
2
votes
3
replies
1.3k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw
R
gage
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
nhwoo
• 0
1
vote
3
replies
1.1k
views
Creating gene set data for yeast
GAGE
gene set
go.gsets
updated 3.7 years ago by
Luo Weijun
★ 1.6k • written 3.7 years ago by
June.
▴ 10
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage
gene set analysis
pathview
kegg
pathway analysis
8.2 years ago
serpalma.v
▴ 60
0
votes
3
replies
1.7k
views
GAGE and PATHVIEW packages
gage
pathview
gage
pathview
updated 10.6 years ago by
Luo Weijun
★ 1.6k • written 10.6 years ago by
Christian De Santis
▴ 150
0
votes
3
replies
1.9k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage
annotationdbi
entrez
ensembl
6.2 years ago
colaneri
▴ 30
0
votes
3
replies
1.5k
views
GAGE: No significant output while it should have
GAGE
updated 6.6 years ago by
Luo Weijun
★ 1.6k • written 6.7 years ago by
littlefishes20
▴ 10
0
votes
2
replies
1.6k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE
pathview
updated 7.3 years ago by
Luo Weijun
★ 1.6k • written 7.4 years ago by
user31888
▴ 30
0
votes
2
replies
982
views
A question about the gage package
Microarray
probe
gage
Microarray
probe
gage
11.1 years ago
He, Yiwen NIH/CIT
▴ 360
0
votes
2
replies
948
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
gage
gage
12.3 years ago
Javerjung Sandhu
▴ 200
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 7.5 years ago by
Michael
• 0
0
votes
2
replies
1.7k
views
Questions about Pathview, maybe also gage
Pathview
Gage
R
updated 7.3 years ago by
bioinf
▴ 10 • written 7.8 years ago by
ChIP-Tease
• 0
0
votes
2
replies
1.5k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE
Cuffdiff
gene names
updated 8.4 years ago by
Luo Weijun
★ 1.6k • written 8.4 years ago by
user31888
▴ 30
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
2
votes
2
replies
1.7k
views
Output from pathview does not seem to match input
pathview
gage
pathway analysis
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
bdp
• 0
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 11 months ago by
Rob
• 0 • written 3.5 years ago by
microPhD
• 0
0
votes
2
replies
1.6k
views
Error when installing package gageData
gage
kegg
6.2 years ago
colaneri
▴ 30
1
vote
2
replies
2.1k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE
Gene Ontology
rna-seq
pathview
updated 6.6 years ago by
Luo Weijun
★ 1.6k • written 6.6 years ago by
JMallory
• 0
0
votes
2
replies
1.3k
views
RNA-seq pathway analysis in Canis familiaris
RNASeq
Genetics
Annotation
Canis familiaris
gage
RNASeq
Genetics
Annotation
gage
updated 9.9 years ago by
James W. MacDonald
65k • written 9.9 years ago by
Jessica Perry Hekman
▴ 140
0
votes
2
replies
1.4k
views
New gage package: Generally Applicable Gene-set/Pathway Analysis
Sequencing
Microarray
Pathways
GO
Yeast
gage
Sequencing
Microarray
Pathways
GO
Yeast
13.5 years ago
Luo Weijun
★ 1.6k
0
votes
2
replies
1.7k
views
retrieve kegg pathway abundances from gage analysis
gage
pathways
kegg
updated 9.1 years ago by
Luo Weijun
★ 1.6k • written 9.2 years ago by
francesca.defilippis
▴ 100
0
votes
2
replies
3.6k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.1 years ago by
Helen
• 0 • written 6.2 years ago by
tarun2
• 0
1
vote
2
replies
1.2k
views
Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.3 years ago by
Emilia
▴ 30
0
votes
1
reply
1.5k
views
GAGE vs other GO analysis tools
Microarray
Pathways
GO
gage
Microarray
Pathways
GO
gage
updated 12.3 years ago by
Luo Weijun
★ 1.6k • written 12.3 years ago by
January Weiner
▴ 240
0
votes
1
reply
1.1k
views
gage package: biological replicates and technical replicates
gage
gage
updated 13.4 years ago by
Luo Weijun
★ 1.6k • written 13.4 years ago by
heyi xiao
▴ 360
0
votes
1
reply
1.9k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 7.0 years ago by
Luo Weijun
★ 1.6k • written 7.0 years ago by
snishtala03
• 0
0
votes
1
reply
1.4k
views
Can GAGE be used for transcript set pathway analysis
Pathways
gage
Pathways
gage
updated 10.0 years ago by
Luo Weijun
★ 1.6k • written 10.0 years ago by
sun
▴ 100
0
votes
1
reply
1.1k
views
A error in GAGE analysis
gage
gage
updated 12.0 years ago by
Luo Weijun
★ 1.6k • written 12.0 years ago by
Javerjung Sandhu
▴ 200
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