Showing : gage • reset
6
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5
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1.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.1 years ago by ★ 1.6k • written 3.1 years ago by • 0
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 ▴ 270 • written 4.7 years ago by ▴ 10
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 50k • written 9.6 years ago by ▴ 120
4
votes
5
replies
1.7k
views
GAGE after tximport
gage tximport
updated 6.4 years ago by ★ 1.6k • written 6.5 years ago by ▴ 230
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
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 65k • written 4.0 years ago by • 0
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 ★ 1.6k • written 8.8 years ago by • 0
2
votes
11
replies
4.4k
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
2
votes
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.4 years ago by ★ 6.8k • written 8.4 years ago by ▴ 30
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.7 years ago by • 0 • written 5.7 years ago by ▴ 40
1
vote
1
reply
916
views
Which group is meant by greater oder less in the gage results?
gage
updated 3.3 years ago by ★ 1.6k • written 3.3 years ago by ▴ 10
1
vote
2
replies
1.1k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 3.3 years ago by ▴ 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
1
vote
3
replies
1.5k
views
DESeq2 rlog as input for GAGE
deseq2 gage
7.8 years ago Tom ▴ 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
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.4 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
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 6.5 years ago by ★ 1.6k • written 6.5 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
10.5 years ago Luo Weijun ★ 1.6k
1
vote
3
replies
1.1k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 3.7 years ago by ★ 1.6k • written 3.7 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 12.2 years ago by ★ 1.6k • written 12.3 years ago by ▴ 240
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 ▴ 200 • written 12.3 years ago by ★ 6.8k
0
votes
0
replies
793
views
equiry about GAGE
Sequencing gage Sequencing gage
13.4 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
895
views
gage
gage gage
12.0 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
947
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
views
GAGE: script
GO gage GO gage
11.5 years ago Guest User ★ 13k
0
votes
2
replies
979
views
A question about the gage package
Microarray probe gage Microarray probe gage
11.1 years ago He, Yiwen NIH/CIT ▴ 360
0
votes
0
replies
894
views
A question about the gage package
Microarray probe gage Microarray probe gage
11.0 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
791
views
sigGeneSet gage function
gage gage
11.0 years ago Vincenzo Capece ▴ 140
0
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0
replies
3.2k
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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
10.7 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.0k
views
GAGE heatmap pdf question...
GO gage GO gage
12.1 years ago Luo Weijun ★ 1.6k
0
votes
0
replies
1.3k
views
GAGE package help required
Pathways gage Pathways gage
12.6 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
1.1k
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
votes
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
845
views
GAGE heatmap pdf question...
GO gage GO gage
12.1 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 12.1 years ago by ▴ 200
0
votes
0
replies
886
views
Biological replicates with Gage
gage gage
12.7 years ago Luo Weijun ★ 1.6k
0
votes
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
replies
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
12.1 years ago Javerjung Sandhu ▴ 200
0
votes
0
replies
649
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
votes
1
reply
1.4k
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 10.3 years ago by ★ 1.6k • written 10.3 years ago by ▴ 100
0
votes
1
reply
1.1k
views
GAGE analysis
Microarray gage Microarray gage
updated 10.3 years ago by ★ 1.6k • written 10.3 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
10.2 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
10.2 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 9.9 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
12.1 years ago Javerjung Sandhu ▴ 200
50 results • Page 1 of 1
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Answer: OrgDb for maize by Guido Hooiveld ★ 3.9k
I notice the data you are working with is based on `ensembl` ids. This is important, because the `OrgDb` are annotation databases that are …
Comment: Theoretical WGCNA Question by Garrett • 0
Thanks Peter!
Comment: FGSEA pre-ranked input in increasing order or decreasing by sropri • 0
Thank you!
Comment: FGSEA pre-ranked input in increasing order or decreasing by alserg ▴ 240
They are reorder in the decreasing order.
Comment: significant difference of p-values with dream() after updating VariancePartition by Le • 0
Thanks for your reply @gabrielhoffman ! I've been trying to isolate the changes, and v1.32.5 had the same results as v1.33.1 while v1.30.0…
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Comment: significant difference of p-values with dream() after updating VariancePartition
How to tell and visualize up/down regulation of pathways from clusterprofiler gsea output
Comment: DEXSeq DEXSeqDataSet count matrix duplication
Comment: Error in champ.load(): The following specified files do not exist
Answer: Error in read.metharray(basenames = files, extended = extended, verbose = verbos
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