Showing : GAGE • reset
0
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13
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2.1k
views
Gage and setp argument
gsea gage
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
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13
replies
5.8k
views
gage pathways enrichment analysis
gage pathways kegg
updated 9.4 years ago by ★ 1.6k • written 9.4 years ago by ▴ 100
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
0
votes
9
replies
3.1k
views
Urgent: Do GAGE applicable for non model species?
gage
updated 8.8 years ago by • 0 • written 8.8 years ago by ▴ 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 ▴ 270 • written 4.7 years ago by ▴ 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 ▴ 470 • written 10.6 years ago by ▴ 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 ★ 1.6k • written 7.9 years ago by • 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 ★ 1.6k • written 9.0 years ago by • 0
6
votes
5
replies
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
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 • 0 • written 5.7 years ago by ▴ 40
4
votes
5
replies
1.7k
views
GAGE after tximport
gage tximport
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by ▴ 230
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
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
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 ▴ 40 • written 7.6 years ago by • 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 ★ 1.2k • written 7.7 years ago by ▴ 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 50k • written 9.6 years ago by ▴ 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 ▴ 230 • written 10.7 years ago by ★ 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 ▴ 200 • written 12.3 years ago by ★ 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 65k • written 4.0 years ago by • 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 ★ 1.6k • written 3.7 years ago by ▴ 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 10.5 years ago by ★ 1.6k • written 10.5 years ago by ▴ 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 6.5 years ago by ★ 1.6k • written 6.7 years ago by ▴ 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 ★ 1.6k • written 7.3 years ago by ▴ 30
0
votes
2
replies
980
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
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
2
replies
1.6k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 7.4 years ago by ★ 1.6k • written 7.5 years ago by • 0
0
votes
2
replies
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
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 ★ 1.6k • written 8.4 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
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
0
votes
2
replies
1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 11 months ago by • 0 • written 3.5 years ago by • 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 6.5 years ago by ★ 1.6k • written 6.5 years ago by • 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 65k • written 9.9 years ago by ▴ 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 ★ 1.6k • written 9.1 years ago by ▴ 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 • 0 • written 6.2 years ago by • 0
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
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
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
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 ★ 1.6k • written 7.0 years ago by • 0
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
1.1k
views
A error in GAGE analysis
gage gage
updated 12.0 years ago by ★ 1.6k • written 12.0 years ago by ▴ 200
50 results • Page 1 of 1
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Answer: Cannabis and KEGGgraph by deeenes ▴ 30
Hello, I'm a developer of the `OmnipathR` package, and I wrote [a function][1] to access certain KEGG data: library(OmnipathR) cs…
Answer: RNAseq:Technical replicates from different batches by Gordon Smyth 50k
I am not entirely clear what you mean by "technical" replicates in this case. Are they resequencing of the same RNA samples or are they fre…
Comment: DMR.Plot shows error "Error in simpleLoess(y, x, w, span, degree = degree, param by russ.bainer ▴ 10
Hi, I'm hitting this too. As far as I can tell my DataTrack is fine, but perhaps I am missing something. Notably the same code works on o…
Comment: The difference when using Limma compare between 3 conditions vs 2 conditions by Chris • 0
Hi Robert, If I don't want to use all pathway in c2 gene set but only a few pathways of interested, how can I do that? So we try to get a …
Comment: How to retrieve detailed regression results from deseq2 by Weiqian ▴ 10
Hi Michael, thanks for the answer! I'll have a look : )
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Installing/switching between versions of R/Rstudio/Bioconductor on personal machine (Linux | Ubuntu)
A: Docker container with bioconductor and devtools
Answer: OrgDb for maize
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
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