Showing : gage • reset
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
6 months ago cereyredondo • 0
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276
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
8 months ago danalvoronov ▴ 10
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1
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854
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 22 months ago by 67k • written 22 months ago by ▴ 10
3
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13
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3.2k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.4 years ago • updated 24 months ago nute11a ▴ 10
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1.0k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.8 years ago OST • 0
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983
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.9 years ago by 43k • written 2.9 years ago by • 0
6
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5
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1.9k
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KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.9 years ago by ★ 1.6k • written 3.9 years ago by • 0
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0
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809
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Setting threshold with gage for gene set analysis
gage gageData
3.9 years ago jd348 • 0
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2
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1.4k
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Can I create a gene set using GAGE?
gage pathview gageData
written 4.0 years ago by ▴ 40
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1
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1.2k
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Which group is meant by greater oder less in the gage results?
gage
updated 4.1 years ago by ★ 1.6k • written 4.1 years ago by ▴ 20
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2
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1.5k
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Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 20 months ago by • 0 • written 4.2 years ago by • 0
1
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3
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1.5k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 4.5 years ago by ★ 1.6k • written 4.5 years ago by ▴ 10
2
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3
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1.8k
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Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 4.8 years ago by 67k • written 4.8 years ago by • 0
0
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0
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1.1k
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gage function problem in R
gage R kegg pathview
updated 5.0 years ago by 43k • written 5.0 years ago by • 0
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0
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1.2k
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
5.3 years ago MimR • 0
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4
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1.5k
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kegg.gsets: unknown species
gage
5.4 years ago mel.p • 0
5
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7
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9.9k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 5.4 years ago by ▴ 280 • written 5.4 years ago by ▴ 10
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1
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1.6k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 20 months ago by • 0 • written 6.3 years ago by • 0
1
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5
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3.4k
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KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 3.5 years ago by • 0 • written 6.5 years ago by ▴ 40
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0
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1.1k
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GAGE for non model organism
gage package gage
6.5 years ago melkile26 • 0
1
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2
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1.4k
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
6.5 years ago atakanekiz ▴ 30
0
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1
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1.6k
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GAGE function and the same.dir option
gage gene set testing
updated 6.7 years ago by ★ 1.6k • written 6.7 years ago by ▴ 20
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2
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4.0k
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Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.9 years ago by • 0 • written 6.9 years ago by • 0
0
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3
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2.3k
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How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
6.9 years ago colaneri ▴ 30
0
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2
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1.9k
views
Error when installing package gageData
gage kegg
7.0 years ago colaneri ▴ 30
0
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0
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1.5k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
7.0 years ago Luo Weijun ★ 1.6k
4
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5
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2.0k
views
GAGE after tximport
gage tximport
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by ▴ 230
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3
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1.8k
views
GAGE: No significant output while it should have
GAGE
updated 7.3 years ago by ★ 1.6k • written 7.4 years ago by ▴ 10
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2
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2.6k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
2
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11
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5.3k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.5 years ago Luo Weijun ★ 1.6k
0
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1
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1.4k
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GAGE: no essential member genes for some DE pathways
gage
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by • 0
0
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1
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2.2k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by • 0
0
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0
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1.3k
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gage pca loadings
pca gage loadings
7.8 years ago MT ▴ 10
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1.4k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.9 years ago avinash gupta ▴ 130
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0
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1.5k
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
7.9 years ago user31888 ▴ 30
0
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4
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2.4k
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Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.1 years ago bioinf ▴ 10
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2
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2.0k
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Questions about Pathview, maybe also gage
Pathview Gage R
updated 8.1 years ago by ▴ 10 • written 8.6 years ago by • 0
0
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2
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1.8k
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by ▴ 30
1
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4
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2.6k
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GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 8.2 years ago by ★ 1.2k • written 8.4 years ago by ▴ 110
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2
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1.8k
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How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 8.2 years ago by ★ 1.6k • written 8.3 years ago by • 0
0
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4
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2.2k
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EGSEA: how does the program generate the value for the up or down regulation of gene sets or pathways
pathways gsea egsea gage
updated 8.3 years ago by ▴ 40 • written 8.3 years ago by • 0
1
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3
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1.7k
views
DESeq2 rlog as input for GAGE
deseq2 gage
8.6 years ago • updated 8.5 years ago Tom ▴ 10
0
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6
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4.3k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 8.6 years ago by ★ 1.6k • written 8.7 years ago by • 0
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13
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2.5k
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Gage and setp argument
gsea gage
8.7 years ago peter.chernek • 0
0
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1
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1.4k
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Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 8.9 years ago by ★ 1.6k • written 8.9 years ago by • 0
1
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3
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1.9k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.9 years ago serpalma.v ▴ 60
0
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2
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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 9.1 years ago by ★ 1.6k • written 9.1 years ago by ▴ 30
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0
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2.4k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
9.2 years ago user31888 ▴ 30
2
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5
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3.2k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.2 years ago by ★ 6.8k • written 9.2 years ago by ▴ 30
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4
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2.6k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
9.4 years ago martin.hoelzer ▴ 20
50 results • Page 1 of 1
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Comment: How to visualize these pathways using pathview by Guido Hooiveld ★ 4.1k
FYI: a similar, if not identical issue has been reported before (`pathview` has problems visualizing some pathways, but not all). You likel…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
I see. Thank you ATpoint!
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by Prakash Sah • 0
Thanks James!
Comment: Why select top highly expressed genes based on normalized counts, but then plot by ATpoint ★ 4.6k
I think I explained what the differences between approach 1 and 2 is in my answer. I assume that the tutorial uses vst because it is varian…
Comment: Why select top highly expressed genes based on normalized counts, but then plot by Quang NN ▴ 10
Thank you ATpoint for your responses. I am a bit confused because the difference between the two approaches is the selection of the genes…
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Comment: can't install tscR
Answer: Csaw normalization strategies - general inquiry
A: DESeq2 interaction term
Comment: Recount3 data correspond to TCGA data
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