Showing : GAGE • reset
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 13 months ago by 65k • written 13 months ago by ▴ 10
3
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13
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2.6k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 15 months ago nute11a ▴ 10
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0
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734
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.1 years ago OST • 0
0
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0
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752
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.2 years ago by 42k • written 2.2 years ago by • 0
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
0
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0
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637
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Setting threshold with gage for gene set analysis
gage gageData
3.2 years ago jd348 • 0
1
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2
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1.2k
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Can I create a gene set using GAGE?
gage pathview gageData
written 3.3 years ago by ▴ 30
1
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1
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932
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Which group is meant by greater oder less in the gage results?
gage
updated 3.4 years ago by ★ 1.6k • written 3.4 years ago by ▴ 10
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2
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1.2k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 12 months ago by • 0 • written 3.5 years ago by • 0
1
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3
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1.2k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 3.7 years ago by ★ 1.6k • written 3.8 years ago by ▴ 10
2
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3
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1.3k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 4.1 years ago by 65k • written 4.1 years ago by • 0
0
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0
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883
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gage function problem in R
gage R kegg pathview
updated 4.3 years ago by 42k • written 4.3 years ago by • 0
0
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0
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958
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
4.5 years ago MimR • 0
0
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4
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1.3k
views
kegg.gsets: unknown species
gage
4.6 years ago mel.p • 0
4
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7
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7.3k
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
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1
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1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 12 months ago by • 0 • written 5.5 years ago by • 0
0
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0
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899
views
GAGE for non model organism
gage package gage
5.8 years ago melkile26 • 0
1
vote
5
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3.0k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 2.8 years ago by • 0 • written 5.8 years ago by ▴ 40
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
0
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1
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1.3k
views
GAGE function and the same.dir option
gage gene set testing
updated 5.9 years ago by ★ 1.6k • written 6.0 years ago by ▴ 20
0
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2
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3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.2 years ago by • 0 • written 6.2 years ago by • 0
0
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3
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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
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2
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1.6k
views
Error when installing package gageData
gage kegg
6.2 years ago colaneri ▴ 30
0
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0
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1.3k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.2 years ago Luo Weijun ★ 1.6k
4
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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
1
vote
2
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2.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by • 0
0
votes
3
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1.6k
views
GAGE: No significant output while it should have
GAGE
updated 6.6 years ago by ★ 1.6k • written 6.7 years ago by ▴ 10
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
6.8 years ago Luo Weijun ★ 1.6k
0
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1
reply
1.2k
views
GAGE: no essential member genes for some DE pathways
gage
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
0
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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
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0
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1.1k
views
gage pca loadings
pca gage loadings
7.1 years ago MT ▴ 10
0
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0
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1.2k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.2 years ago avinash gupta ▴ 130
0
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0
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1.3k
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
7.2 years ago user31888 ▴ 30
0
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4
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2.0k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
7.3 years ago bioinf ▴ 10
0
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2
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1.6k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 7.4 years ago by ★ 1.6k • written 7.4 years ago by ▴ 30
0
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2
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1.6k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 7.5 years ago by ★ 1.6k • written 7.6 years ago by • 0
0
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4
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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
1
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4
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2.3k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 7.5 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
1
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3
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1.5k
views
DESeq2 rlog as input for GAGE
deseq2 gage
7.8 years ago Tom ▴ 10
0
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2
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1.7k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.4 years ago by ▴ 10 • written 7.8 years ago by • 0
0
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6
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3.5k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 7.9 years ago by ★ 1.6k • written 8.0 years ago by • 0
0
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13
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2.2k
views
Gage and setp argument
gsea gage
8.0 years ago peter.chernek • 0
0
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1
reply
1.2k
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 8.2 years ago by ★ 1.6k • written 8.2 years ago by • 0
1
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3
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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
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2
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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
0
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0
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2.2k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
8.5 years ago user31888 ▴ 30
2
votes
5
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2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 8.5 years ago by ★ 6.8k • written 8.5 years ago by ▴ 30
0
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4
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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
0
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0
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1.2k
views
Detail of GAGE's esset.grp function
gage
8.7 years ago jackipchiho ▴ 10
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
50 results • Page 1 of 1
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Comment: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it by Hervé Pagès 16k
Indeed. Calculations involving floating point arithmetic are architecture-dependent, and testing the results should be done with `all.equal…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Poonam • 0
I will follow what you suggested. I didn't use max gap anywhere. I was following statistic I and regarding the size of features, my small…
Comment: How to use bootRanges to bootstrap small RNA loci (nullranges package) by Michael Love 42k
Oh I see, for the second question, I don't have a great answer. I typically think of one set as the anchor, whose ascertainment is driving …
Comment: Help with running egsea() by James W. MacDonald 65k
Oh, right. Ideally you would use NCBI (aka Entrez gene) IDs because they are way more likely to be unique. Gene symbols are broken down int…
Comment: Help with running egsea() by Chris • 0
Thanks James! I update the question. The last question mean when we use `buildIdx()`, could we use gene symbol instead of entrezID. However…
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Answer: How to save the DEXSeq results
Answer: minfi support of illumina Infinium methylationEPIC v2.0
Comment: minfi support of illumina Infinium methylationEPIC v2.0
Answer: Mac ARM64 build report for BioC 3.19 from 'kjohnson3' reporting ERROR which it
Comment: Help with running egsea()
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