Showing : GAGE • reset
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GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
10.0 years ago martin.hoelzer ▴ 20
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0
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1.4k
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Detail of GAGE's esset.grp function
gage
10.1 years ago jackipchiho ▴ 10
2
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2
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2.1k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by • 0
0
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0
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1.7k
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How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
10.2 years ago jackipchiho ▴ 10
0
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9
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3.9k
views
Urgent: Do GAGE applicable for non model species?
gage
updated 10.2 years ago by • 0 • written 10.2 years ago by ▴ 10
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1
reply
1.7k
views
GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)
GO gage pathview GO gage pathview
updated 10.2 years ago by ▴ 10 • written 11.3 years ago by ★ 1.6k
0
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6
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3.4k
views
Gene set enrichment analysis with gage package returning NaN p-values
gage gsea rnaseq
updated 10.4 years ago by ★ 1.6k • written 10.4 years ago by • 0
0
votes
2
replies
2.2k
views
retrieve kegg pathway abundances from gage analysis
gage pathways kegg
updated 10.6 years ago by ★ 1.6k • written 10.6 years ago by ▴ 100
0
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13
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7.0k
views
gage pathways enrichment analysis
gage pathways kegg
updated 10.8 years ago by ★ 1.6k • written 10.8 years ago by ▴ 100
4
votes
4
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9.1k
views
Packages for GO and KEGG analysis on RNAseq data
GO gage goseq KEGG
updated 10.9 years ago by 53k • written 11.0 years ago by ▴ 120
0
votes
0
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2.1k
views
questions about gage
gage DESeq2 gage DESeq2
11.1 years ago Luo Weijun ★ 1.6k
0
votes
0
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1.9k
views
GAGE/Pathview analysis data preparation
GO gage pathview GO gage pathview
11.1 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
2.0k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Annotation Normalization gage pathview Transcription Annotation Normalization
updated 11.2 years ago by ▴ 20 • written 11.2 years ago by ★ 1.6k
0
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0
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1.4k
views
An. Gambie RNA-Seq differential expression using gage and pathview
Transcription Normalization gage Transcription Normalization gage
11.2 years ago Saul Lozano ▴ 20
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0
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1.2k
views
Pathview plot split by experiment condition
gage pathview gage pathview
11.3 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.5k
views
RNA-seq pathway analysis in Canis familiaris
RNASeq Genetics Annotation Canis familiaris gage RNASeq Genetics Annotation gage
updated 11.4 years ago by 68k • written 11.4 years ago by ▴ 140
0
votes
1
reply
1.7k
views
Can GAGE be used for transcript set pathway analysis
Pathways gage Pathways gage
updated 11.4 years ago by ★ 1.6k • written 11.4 years ago by ▴ 100
0
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0
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1.3k
views
Update in the gage RNA-seq pathway analysis joint workflow
limma edgeR gage limma edgeR gage
11.6 years ago Luo Weijun ★ 1.6k
0
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0
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2.4k
views
Pathview with minor species
Microarray Annotation GO Bacillus subtilis gage pathview Microarray Annotation GO gage
11.6 years ago Luo Weijun ★ 1.6k
0
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0
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1.5k
views
Pathview with minor species
Microarray Annotation Bacillus subtilis gage pathview Microarray Annotation gage pathview
11.6 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
2.7k
views
gage and GO analysis
GO convert gage GO convert gage
updated 11.7 years ago by ▴ 570 • written 11.7 years ago by ★ 13k
0
votes
1
reply
1.3k
views
GAGE analysis
Microarray gage Microarray gage
updated 11.7 years ago by ★ 1.6k • written 11.7 years ago by ▴ 130
0
votes
5
replies
2.8k
views
Rgraphviz installation issue
Rgraphviz gage Rgraphviz gage
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by ▴ 100
0
votes
1
reply
1.7k
views
Can gage not use large gene sets for pathway analysis?
Pathways gage pathview Pathways gage pathview
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by ★ 13k
0
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0
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1.2k
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Redundant gene sets & gagePipe
gage gage
11.8 years ago Luo Weijun ★ 1.6k
0
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0
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805
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Redundant gene sets & gagePipe
gage gage
11.8 years ago Christian De Santis ▴ 150
0
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1
reply
1.6k
views
gage function---kegg.gsets
gage gage
updated 11.8 years ago by ★ 1.6k • written 11.8 years ago by ★ 13k
0
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0
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3.4k
views
DESeq2 with GAGE
Pathways cycle gage DESeq2 pathview Pathways cycle gage DESeq2 pathview
11.9 years ago Luo Weijun ★ 1.6k
1
vote
0
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2.0k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization gage pathview Visualization gage pathview
11.9 years ago Luo Weijun ★ 1.6k
0
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3
replies
2.1k
views
GAGE and PATHVIEW packages
gage pathview gage pathview
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 150
0
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1
reply
3.3k
views
GAGE/Pathview RNA-Seq Data Pathway and Gene-set Analysis Workflows
GO Visualization edgeR gage GO Visualization edgeR gage
12.0 years ago Luo Weijun ★ 1.6k
0
votes
7
replies
5.4k
views
Simple pathway enrichment analysis for gene lists
Microarray Category gage KEGGREST ROntoTools Microarray Category gage KEGGREST ROntoTools
updated 12.0 years ago by ▴ 470 • written 12.0 years ago by ▴ 680
0
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0
replies
886
views
enrichment packages that accept t-stat (or related stat) as input
limma gage limma gage
12.1 years ago Luo Weijun ★ 1.6k
0
votes
4
replies
3.9k
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 12.1 years ago by ▴ 230 • written 12.1 years ago by ★ 1.6k
0
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0
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3.1k
views
Pathview with non-KEGG organisms?
Microbiome Pathways GO Visualization Organism graph gage pathview Microbiome Pathways GO
12.1 years ago Luo Weijun ★ 1.6k
0
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0
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3.5k
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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
12.2 years ago Luo Weijun ★ 1.6k
0
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0
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996
views
sigGeneSet gage function
gage gage
12.4 years ago Vincenzo Capece ▴ 140
0
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0
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1.1k
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A question about the gage package
Microarray probe gage Microarray probe gage
12.5 years ago Luo Weijun ★ 1.6k
0
votes
2
replies
1.2k
views
A question about the gage package
Microarray probe gage Microarray probe gage
12.5 years ago He, Yiwen NIH/CIT ▴ 360
0
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0
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1.3k
views
GAGE: script
GO gage GO gage
12.9 years ago Guest User ★ 13k
0
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1
reply
1.4k
views
A error in GAGE analysis
gage gage
updated 13.4 years ago by ★ 1.6k • written 13.4 years ago by ▴ 200
0
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0
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1.1k
views
gage
gage gage
13.4 years ago Luo Weijun ★ 1.6k
0
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1
reply
1.3k
views
GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
convert gage convert gage
updated 13.5 years ago by ★ 1.6k • written 13.6 years ago by ▴ 200
0
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0
replies
1.2k
views
GAGE heatmap pdf question...
GO gage GO gage
13.5 years ago Luo Weijun ★ 1.6k
0
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0
replies
1.0k
views
GAGE heatmap pdf question...
GO gage GO gage
13.6 years ago Alan Derr ▴ 50
0
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0
replies
1.3k
views
GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa
convert gage convert gage
13.6 years ago Javerjung Sandhu ▴ 200
0
votes
1
reply
1.1k
views
GAGE heatmap pdf question...
gage gage
13.6 years ago Alan Derr ▴ 50
0
votes
1
reply
1.4k
views
GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
convert gage convert gage
13.6 years ago Javerjung Sandhu ▴ 200
0
votes
0
replies
972
views
GAGE Question
probe biomaRt gage probe biomaRt gage
13.6 years ago Javerjung Sandhu ▴ 200
0
votes
1
reply
1.3k
views
Error in GAGE analysis, help URGENTLY required
gage gage
13.6 years ago Javerjung Sandhu ▴ 200
114 results • Page 2 of 3
Recent ...
Replies
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Exactly, MDS was computed on logCPM values from `cpm(x, log=TRUE)` after running `calcNormFactors(method="TMMwsp")` on the DGE object. I al…
Answer: GO.db and others package Download failure by James W. MacDonald 68k
You didn't get an error. You didn't even get a warning! You simply got a message saying that two (unrelated) packages were not updated. As …
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by Gordon Smyth 53k
MDS of what quantity? LogCPM from `cpm()`? I don't have a definitive answer, but my feeling that is that library size effects are to be ex…
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design by abaed • 0
Apologies for not clarifying earlier, you're right: it is a PCA, not an MDS. In local machine, computing the MDS takes quite a long time, P…
Answer: replace cat with message in glmTreat when lfc = 0 by Gordon Smyth 53k
Yes, I agree that the message should be a `message` rather than `cat` output, and the message is perhaps not needed at all, because anyone …
Votes
Comment: readDNAStringSet with non DNA characters
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Answer: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
Comment: Guidance on limma for pseudobulk scRNA-seq with multi-factor design
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