Showing : GAGE • reset
6
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5
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KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
4
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7
replies
7.3k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 4.7 years ago by ▴ 270 • written 4.7 years ago by ▴ 10
4
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4
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7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 9.5 years ago by 50k • written 9.6 years ago by ▴ 120
4
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5
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1.7k
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GAGE after tximport
gage tximport
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by ▴ 230
3
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13
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2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
2
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3
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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 65k • written 4.0 years ago by • 0
2
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2
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1.7k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.8 years ago Luo Weijun ★ 1.6k
2
votes
5
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2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ▴ 30
1
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5
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3.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.8 years ago by • 0 • written 5.8 years ago by ▴ 40
1
vote
1
reply
928
views
Which group is meant by greater oder less in the gage results?
gage
updated 3.4 years ago by ★ 1.6k • written 3.4 years ago by ▴ 10
1
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2
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1.2k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 3.3 years ago by ▴ 30
1
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2
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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
1
vote
3
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1.5k
views
DESeq2 rlog as input for GAGE
deseq2 gage
7.8 years ago Tom ▴ 10
1
vote
3
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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
1
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4
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2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.5 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
1
vote
2
replies
2.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by • 0
1
vote
0
replies
1.7k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
10.6 years ago Luo Weijun ★ 1.6k
1
vote
3
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1.2k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 3.7 years ago by ★ 1.6k • written 3.8 years ago by ▴ 10
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 ★ 1.6k • written 12.3 years ago by ▴ 240
0
votes
3
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2.4k
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 ▴ 200 • written 12.3 years ago by ★ 6.8k
0
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0
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796
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equiry about GAGE
Sequencing gage Sequencing gage
13.4 years ago Luo Weijun ★ 1.6k
0
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0
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901
views
gage
gage gage
12.0 years ago Luo Weijun ★ 1.6k
0
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2
replies
951
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
1
reply
1.1k
views
A error in GAGE analysis
gage gage
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 200
0
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0
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1.1k
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GAGE: script
GO gage GO gage
11.5 years ago Guest User ★ 13k
0
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2
replies
985
views
A question about the gage package
Microarray probe gage Microarray probe gage
11.1 years ago He, Yiwen NIH/CIT ▴ 360
0
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0
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902
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A question about the gage package
Microarray probe gage Microarray probe gage
11.1 years ago Luo Weijun ★ 1.6k
0
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0
replies
800
views
sigGeneSet gage function
gage gage
11.0 years ago Vincenzo Capece ▴ 140
0
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0
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Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation Pathways Visualization graph PROcess gage pathview Annotation Pathways graph
10.8 years ago Luo Weijun ★ 1.6k
0
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0
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1.0k
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GAGE heatmap pdf question...
GO gage GO gage
12.1 years ago Luo Weijun ★ 1.6k
0
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0
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1.3k
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GAGE package help required
Pathways gage Pathways gage
12.7 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.2k
views
gage package: biological replicates and technical replicates
gage gage
updated 13.4 years ago by ★ 1.6k • written 13.4 years ago by ▴ 360
0
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2
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1.7k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.3 years ago by ▴ 10 • written 7.8 years ago by • 0
0
votes
0
replies
852
views
GAGE heatmap pdf question...
GO gage GO gage
12.2 years ago Alan Derr ▴ 50
0
votes
1
reply
1.1k
views
GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
convert gage convert gage
updated 12.1 years ago by ★ 1.6k • written 12.2 years ago by ▴ 200
0
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0
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896
views
Biological replicates with Gage
gage gage
12.7 years ago Luo Weijun ★ 1.6k
0
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0
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1.0k
views
Redundant gene sets & gagePipe
gage gage
10.4 years ago Luo Weijun ★ 1.6k
0
votes
0
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1.1k
views
GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa
convert gage convert gage
12.2 years ago Javerjung Sandhu ▴ 200
0
votes
0
replies
653
views
Redundant gene sets & gagePipe
gage gage
10.4 years ago Christian De Santis ▴ 150
0
votes
1
reply
1.3k
views
gage function---kegg.gsets
gage gage
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ★ 13k
0
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1
reply
1.5k
views
Can gage not use large gene sets for pathway analysis?
Pathways gage pathview Pathways gage pathview
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ★ 13k
0
votes
5
replies
2.3k
views
Rgraphviz installation issue
Rgraphviz gage Rgraphviz gage
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 100
0
votes
1
reply
1.1k
views
GAGE analysis
Microarray gage Microarray gage
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by ▴ 130
0
votes
1
reply
2.4k
views
gage and GO analysis
GO convert gage GO convert gage
updated 10.3 years ago by ▴ 570 • written 10.3 years ago by ★ 13k
0
votes
0
replies
1.3k
views
Pathview with minor species
Microarray Annotation Bacillus subtilis gage pathview Microarray Annotation gage pathview
10.3 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
2.1k
views
Pathview with minor species
Microarray Annotation GO Bacillus subtilis gage pathview Microarray Annotation GO gage
10.3 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.1k
views
Update in the gage RNA-seq pathway analysis joint workflow
limma edgeR gage limma edgeR gage
10.2 years ago Luo Weijun ★ 1.6k
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 ★ 1.6k • written 10.0 years ago by ▴ 100
0
votes
1
reply
1.0k
views
GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
convert gage convert gage
12.2 years ago Javerjung Sandhu ▴ 200
50 results • Page 1 of 1
Recent ...
Replies
Comment: Once again a "Model matrix not full rank" by James W. MacDonald 65k
In that case both time and treatment are identical things, so choose one and go with it.
Comment: Once again a "Model matrix not full rank" by arfranco ▴ 130
numbers 1 to 3 represent observations and/or replicates Control is control. The three controls are shown as Control_1, control_2 and Contr…
Answer: Once again a "Model matrix not full rank" by James W. MacDonald 65k
The time and treatment are essentially the same thing, so you cannot have both in the model at the same time. Do the numbers 1:3 represent …
Answer: DESeq2 v1.35.0 by Michael Love 41k
That is not a release (odd 'y' digit). See Bioconductor help pages: https://contributions.bioconductor.org/description.html#description-ver…
Comment: Although I successfully installed the package "simpleaffy'' , I cannot library i by James W. MacDonald 65k
Please don't piggyback on posts from 2.3 years ago. If you have a question, post as a new question.
Votes
Bioconductor 3.19 is Released!
A: Error in DESeqDataSet : some values in assay are not integers
Bioconductor 3.19 is Released!
Bioconductor 3.19 is Released!
Answer: DEseq2 coefficient
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