Showing : GAGE • reset
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
4 months ago cereyredondo • 0
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0
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231
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
6 months ago danalvoronov ▴ 10
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1
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808
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 20 months ago by 67k • written 20 months ago by ▴ 10
3
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13
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3.1k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.3 years ago • updated 21 months ago nute11a ▴ 10
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957
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.6 years ago OST • 0
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923
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.7 years ago by 42k • written 2.7 years ago by • 0
6
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5
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1.8k
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KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.7 years ago by ★ 1.6k • written 3.7 years ago by • 0
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0
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775
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Setting threshold with gage for gene set analysis
gage gageData
3.7 years ago jd348 • 0
1
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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 3.9 years ago by ▴ 40
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1
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1.1k
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Which group is meant by greater oder less in the gage results?
gage
updated 3.9 years ago by ★ 1.6k • written 3.9 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 18 months ago by • 0 • written 4.0 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 4.3 years ago by ★ 1.6k • written 4.3 years ago by ▴ 10
2
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3
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1.7k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 4.6 years ago by 67k • written 4.6 years ago by • 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 4.8 years ago by 42k • written 4.8 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
5.1 years ago MimR • 0
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4
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1.5k
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kegg.gsets: unknown species
gage
5.2 years ago mel.p • 0
5
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7
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9.3k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 5.3 years ago by ▴ 280 • written 5.3 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 18 months ago by • 0 • written 6.1 years ago by • 0
1
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5
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3.3k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 3.3 years ago by • 0 • written 6.3 years ago by ▴ 40
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0
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1.0k
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GAGE for non model organism
gage package gage
6.3 years ago melkile26 • 0
1
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2
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1.3k
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
6.4 years ago atakanekiz ▴ 30
0
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1
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1.5k
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GAGE function and the same.dir option
gage gene set testing
updated 6.5 years ago by ★ 1.6k • written 6.5 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 2.7 years ago by • 0 • written 6.8 years ago by • 0
0
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3
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2.2k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
6.8 years ago colaneri ▴ 30
0
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2
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1.8k
views
Error when installing package gageData
gage kegg
6.8 years ago colaneri ▴ 30
0
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0
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1.4k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.8 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 7.0 years ago by ★ 1.6k • written 7.1 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 7.1 years ago by ★ 1.6k • written 7.2 years ago by ▴ 10
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2
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2.5k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by • 0
2
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11
replies
5.1k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.3 years ago Luo Weijun ★ 1.6k
0
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1
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1.3k
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GAGE: no essential member genes for some DE pathways
gage
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by • 0
0
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1
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2.1k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
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0
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1.3k
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gage pca loadings
pca gage loadings
7.6 years ago MT ▴ 10
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1.4k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.7 years ago avinash gupta ▴ 130
0
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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
7.8 years ago user31888 ▴ 30
0
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4
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2.3k
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Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
7.9 years ago bioinf ▴ 10
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2
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1.9k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.9 years ago by ▴ 10 • written 8.4 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 7.9 years ago by ★ 1.6k • written 7.9 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 8.0 years ago by ★ 1.2k • written 8.2 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 8.0 years ago by ★ 1.6k • written 8.1 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 8.2 years ago by ▴ 40 • written 8.2 years ago by • 0
1
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3
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1.7k
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DESeq2 rlog as input for GAGE
deseq2 gage
8.4 years ago Tom ▴ 10
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6
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4.2k
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Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 8.4 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
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13
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2.5k
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Gage and setp argument
gsea gage
8.5 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 8.7 years ago by ★ 1.6k • written 8.7 years ago by • 0
1
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3
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1.8k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.8 years ago • updated 8.7 years ago serpalma.v ▴ 60
0
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2
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1.7k
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GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 9.0 years ago by ★ 1.6k • written 9.0 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
9.0 years ago user31888 ▴ 30
2
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5
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3.1k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.0 years ago by ★ 6.8k • written 9.0 years ago by ▴ 30
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4
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2.5k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
9.2 years ago martin.hoelzer ▴ 20
50 results • Page 1 of 1
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Answer: DE analysis on Single cell RNA Seq time course data (using pseudotime) with 5 di by James W. MacDonald 67k
The two contrasts at the bottom are identical but for the sign of the logFC, so you should expect the same results (except for flipped sign…
Comment: Identical samples after deseq2 batch effect removal by Michael Love 42k
Oh, i didn't realize there is another method in the mix here. I would not necessarily trust this "batch correction" method, and suspect o…
Comment: Identifying potentially associated gene set to drug response using GSVA by Kent • 0
Hi @robertc thanks for the reply. I should have explained to you the context first. I am testing over a hundred drugs on patient samples (s…
Answer: BiocNeighbours Utility for k-Nearest Neighbour Classification by James W. MacDonald 67k
You can easily answer this question yourself. ``` > library(BiocPkgTools) Loading required package: htmlwidgets > depdf <- buildPkgDe…
Answer: HilBertVis install error by James W. MacDonald 67k
It appears you have compiler flags set that preclude you from compiling (-Werror=format-security). If I install `HilbertVis` on my work box…
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A: Error in DESeqDataSet : some values in assay are not integers
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A: Using of limma moderated t-test with "corrected" expression matrix resulting fr
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