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Showing :
GAGE
•
reset
0
votes
0
replies
307
views
How to use GAGE with my own metagenomic KOFams data
kegg.gsets
gageData
gage
KEGG
4 months ago
cereyredondo
• 0
0
votes
0
replies
244
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
6 months ago
danalvoronov
▴ 10
0
votes
1
reply
819
views
what does "exp1" mean in the gage() function?
gage
clusterProfiler
DESeq2
updated 20 months ago by
James W. MacDonald
67k • written 20 months ago by
m-bihie
▴ 10
3
votes
13
replies
3.1k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
2.3 years ago • updated 22 months ago
nute11a
▴ 10
0
votes
0
replies
972
views
Pathway Analysis using GAGE
gage
RNASeq
gageData
Pathways
2.7 years ago
OST
• 0
0
votes
0
replies
937
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage
plot
RNASeq
goseq
updated 2.7 years ago by
Michael Love
43k • written 2.8 years ago by
m.glymenaki
• 0
6
votes
5
replies
1.8k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.7 years ago by
Luo Weijun
★ 1.6k • written 3.7 years ago by
MOHAMMAD
• 0
0
votes
0
replies
782
views
Setting threshold with gage for gene set analysis
gage
gageData
3.7 years ago
jd348
• 0
1
vote
2
replies
1.4k
views
Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.9 years ago by
Emilia
▴ 40
1
vote
1
reply
1.1k
views
Which group is meant by greater oder less in the gage results?
gage
updated 4.0 years ago by
Luo Weijun
★ 1.6k • written 4.0 years ago by
Matthias Munz
▴ 20
0
votes
2
replies
1.5k
views
Pathway analysis using GAGE returns all NA values
gage
rna-seq
pathwayanalysis
updated 19 months ago by
Rob
• 0 • written 4.1 years ago by
microPhD
• 0
1
vote
3
replies
1.5k
views
Creating gene set data for yeast
GAGE
gene set
go.gsets
updated 4.3 years ago by
Luo Weijun
★ 1.6k • written 4.4 years ago by
June.
▴ 10
2
votes
3
replies
1.7k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw
R
gage
updated 4.6 years ago by
James W. MacDonald
67k • written 4.6 years ago by
nhwoo
• 0
0
votes
0
replies
1.1k
views
gage function problem in R
gage
R
kegg
pathview
updated 4.9 years ago by
Michael Love
43k • written 4.9 years ago by
eozcan
• 0
0
votes
0
replies
1.2k
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage
pathview
KEGG
Gene enrichment analysis
5.1 years ago
MimR
• 0
0
votes
4
replies
1.5k
views
kegg.gsets: unknown species
gage
5.2 years ago
mel.p
• 0
5
votes
7
replies
9.5k
views
Comparison between two different group's pathway analysis results
gage
DESeq2
pathway analysis
updated 5.3 years ago by
mikhael.manurung
▴ 280 • written 5.3 years ago by
tntntntntn
▴ 10
0
votes
1
reply
1.6k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG
GAGE
NaN
R
DESeq2
updated 19 months ago by
Rob
• 0 • written 6.1 years ago by
owen.donohoe
• 0
1
vote
5
replies
3.3k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 3.4 years ago by
najib
• 0 • written 6.4 years ago by
bekah
▴ 40
0
votes
0
replies
1.0k
views
GAGE for non model organism
gage package
gage
6.4 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
0
votes
1
reply
1.5k
views
GAGE function and the same.dir option
gage
gene set testing
updated 6.5 years ago by
Luo Weijun
★ 1.6k • written 6.5 years ago by
Aurora
▴ 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 2.8 years ago by
Helen
• 0 • written 6.8 years ago by
tarun2
• 0
0
votes
3
replies
2.2k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage
annotationdbi
entrez
ensembl
6.8 years ago
colaneri
▴ 30
0
votes
2
replies
1.8k
views
Error when installing package gageData
gage
kegg
6.8 years ago
colaneri
▴ 30
0
votes
0
replies
1.4k
views
pathview and gage server connection issue
pathview
gage
pathway analysis
kegg
visualization
6.8 years ago
Luo Weijun
★ 1.6k
4
votes
5
replies
2.0k
views
GAGE after tximport
gage
tximport
updated 7.1 years ago by
Luo Weijun
★ 1.6k • written 7.1 years ago by
Ed Siefker
▴ 230
0
votes
3
replies
1.8k
views
GAGE: No significant output while it should have
GAGE
updated 7.2 years ago by
Luo Weijun
★ 1.6k • written 7.3 years ago by
littlefishes20
▴ 10
1
vote
2
replies
2.5k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE
Gene Ontology
rna-seq
pathview
updated 7.2 years ago by
Luo Weijun
★ 1.6k • written 7.2 years ago by
JMallory
• 0
2
votes
11
replies
5.1k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
7.4 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.3k
views
GAGE: no essential member genes for some DE pathways
gage
updated 7.6 years ago by
Luo Weijun
★ 1.6k • written 7.6 years ago by
aurelie.nicolas
• 0
0
votes
1
reply
2.1k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R
GSEA
GAGE
pathways
updated 7.6 years ago by
Luo Weijun
★ 1.6k • written 7.6 years ago by
snishtala03
• 0
0
votes
0
replies
1.3k
views
gage pca loadings
pca
gage
loadings
7.7 years ago
MT
▴ 10
0
votes
0
replies
1.4k
views
Pathway analysis for diffrential express gene
pathways
gage
annotation
gostats
7.8 years ago
avinash gupta
▴ 130
0
votes
0
replies
1.5k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage
deseq
pathview
7.8 years ago
user31888
▴ 30
0
votes
4
replies
2.3k
views
Error: Pathway analysis using Sleuth results
pathview
gage
rna-seq
R
sleuth
7.9 years ago
bioinf
▴ 10
0
votes
2
replies
1.9k
views
Questions about Pathview, maybe also gage
Pathview
Gage
R
updated 7.9 years ago by
bioinf
▴ 10 • written 8.4 years ago by
ChIP-Tease
• 0
0
votes
2
replies
1.8k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE
pathview
updated 8.0 years ago by
Luo Weijun
★ 1.6k • written 8.0 years ago by
user31888
▴ 30
1
vote
4
replies
2.6k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 8.1 years ago by
Guangchuang Yu
★ 1.2k • written 8.3 years ago by
rubi
▴ 110
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 8.2 years ago by
Michael
• 0
0
votes
4
replies
2.2k
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 8.2 years ago by
Monther Alhamdoosh
▴ 40 • written 8.2 years ago by
yingchen
• 0
1
vote
3
replies
1.7k
views
DESeq2 rlog as input for GAGE
deseq2
gage
8.4 years ago
Tom
▴ 10
0
votes
6
replies
4.2k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage
pathview
error
updated 8.5 years ago by
Luo Weijun
★ 1.6k • written 8.5 years ago by
marie.bordone
• 0
0
votes
13
replies
2.5k
views
Gage and setp argument
gsea
gage
8.6 years ago
peter.chernek
• 0
0
votes
1
reply
1.4k
views
Using Gage and pathview with previously processed data
pathview
gage
r
kegg
rnaseq
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
bsguida
• 0
1
vote
3
replies
1.8k
views
Discrepancy in gene set size between gage() and geneData()
gage
gene set analysis
pathview
kegg
pathway analysis
8.8 years ago
serpalma.v
▴ 60
0
votes
2
replies
1.7k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE
Cuffdiff
gene names
updated 9.0 years ago by
Luo Weijun
★ 1.6k • written 9.0 years ago by
user31888
▴ 30
0
votes
0
replies
2.4k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE
libpn
9.0 years ago
user31888
▴ 30
2
votes
5
replies
3.2k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps
GAGE
updated 9.1 years ago by
Valerie Obenchain
★ 6.8k • written 9.1 years ago by
user31888
▴ 30
0
votes
4
replies
2.6k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage
pathview
9.2 years ago
martin.hoelzer
▴ 20
50 results • Page
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Thank you for your detailed answer, I appreciate it and your work.
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