Showing : gage • reset
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533
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GAGE kegg.gsets() self-signed certificate error
gageData gage
10 months ago Lucas • 0
0
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0
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646
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
19 months ago cereyredondo • 0
0
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0
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555
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
21 months ago danalvoronov ▴ 10
0
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1
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1.1k
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 2.9 years ago by 68k • written 2.9 years ago by ▴ 10
3
votes
13
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4.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.5 years ago • updated 3.0 years ago nute11a ▴ 10
0
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0
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1.2k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.8 years ago OST • 0
0
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0
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1.3k
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3.9 years ago by 43k • written 3.9 years ago by • 0
6
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5
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2.5k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.9 years ago by ★ 1.6k • written 4.9 years ago by • 0
0
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0
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980
views
Setting threshold with gage for gene set analysis
gage gageData
4.9 years ago jd348 • 0
1
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2
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1.8k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 5.1 years ago by ▴ 40
1
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1
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1.4k
views
Which group is meant by greater oder less in the gage results?
gage
updated 5.1 years ago by ★ 1.6k • written 5.1 years ago by ▴ 20
0
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2
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1.8k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 2.7 years ago by • 0 • written 5.3 years ago by • 0
1
vote
3
replies
1.9k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 5.5 years ago by ★ 1.6k • written 5.5 years ago by ▴ 10
2
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3
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2.4k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 5.8 years ago by 68k • written 5.8 years ago by • 0
0
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0
replies
1.4k
views
gage function problem in R
gage R kegg pathview
updated 6.0 years ago by 43k • written 6.0 years ago by • 0
0
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0
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1.6k
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
6.3 years ago MimR • 0
0
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4
replies
2.0k
views
kegg.gsets: unknown species
gage
6.4 years ago mel.p • 0
5
votes
7
replies
12k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 6.5 years ago by ▴ 280 • written 6.5 years ago by ▴ 10
0
votes
1
reply
1.9k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 2.7 years ago by • 0 • written 7.3 years ago by • 0
1
vote
5
replies
4.1k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.6 years ago by • 0 • written 7.5 years ago by ▴ 40
0
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0
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1.3k
views
GAGE for non model organism
gage package gage
7.5 years ago melkile26 • 0
1
vote
2
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1.7k
views
GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
7.6 years ago atakanekiz ▴ 30
0
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1
reply
1.9k
views
GAGE function and the same.dir option
gage gene set testing
updated 7.7 years ago by ★ 1.6k • written 7.7 years ago by ▴ 20
0
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2
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4.8k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 3.9 years ago by • 0 • written 8.0 years ago by • 0
0
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3
replies
2.6k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
8.0 years ago colaneri ▴ 30
0
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2
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2.2k
views
Error when installing package gageData
gage kegg
8.0 years ago colaneri ▴ 30
0
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0
replies
1.7k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
8.0 years ago Luo Weijun ★ 1.6k
4
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5
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2.4k
views
GAGE after tximport
gage tximport
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by ▴ 230
0
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3
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2.2k
views
GAGE: No significant output while it should have
GAGE
updated 8.3 years ago by ★ 1.6k • written 8.5 years ago by ▴ 10
1
vote
2
replies
3.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 8.3 years ago by ★ 1.6k • written 8.3 years ago by • 0
2
votes
11
replies
6.2k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
8.6 years ago • updated 8.5 years ago Luo Weijun ★ 1.6k
0
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1
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1.6k
views
GAGE: no essential member genes for some DE pathways
gage
updated 8.7 years ago by ★ 1.6k • written 8.7 years ago by • 0
0
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1
reply
2.6k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
0
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0
replies
1.5k
views
gage pca loadings
pca gage loadings
8.8 years ago MT ▴ 10
0
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0
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1.7k
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.9 years ago avinash gupta ▴ 130
0
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0
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1.7k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
9.0 years ago user31888 ▴ 30
0
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4
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2.8k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
9.1 years ago bioinf ▴ 10
0
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2
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2.3k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 9.1 years ago by ▴ 10 • written 9.6 years ago by • 0
0
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2
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2.1k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 9.1 years ago by ★ 1.6k • written 9.1 years ago by ▴ 30
1
vote
4
replies
3.2k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 9.2 years ago by ★ 1.2k • written 9.5 years ago by ▴ 110
0
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2
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2.2k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 9.2 years ago by ★ 1.6k • written 9.3 years ago by • 0
0
votes
4
replies
2.7k
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 9.4 years ago by ▴ 40 • written 9.4 years ago by • 0
1
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3
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2.0k
views
DESeq2 rlog as input for GAGE
deseq2 gage
9.6 years ago Tom ▴ 10
0
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6
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5.0k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 9.6 years ago by ★ 1.6k • written 9.7 years ago by • 0
0
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13
replies
3.3k
views
Gage and setp argument
gsea gage
9.7 years ago peter.chernek • 0
0
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1
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1.6k
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 10.0 years ago by ★ 1.6k • written 10.0 years ago by • 0
1
vote
3
replies
2.3k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
10.0 years ago serpalma.v ▴ 60
0
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2
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2.0k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 10.2 years ago by ★ 1.6k • written 10.2 years ago by ▴ 30
0
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0
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2.7k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
10.2 years ago user31888 ▴ 30
2
votes
5
replies
3.7k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 10.2 years ago by ★ 6.8k • written 10.2 years ago by ▴ 30
114 results • Page 1 of 3
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Comment: soGGi error by shepherl 4.3k
We have tried to contact the soGGi maintainer to have them update the package to the newer version of gglot2 but they have so far been unre…
Comment: using limma trend workflow in CAMERA by Gordon Smyth 53k
No, `trend.var=TRUE` and `trend=TRUE` are not needed in any voom pipeline, because the trend is already incorporated into the voom weights.
Comment: Questions about bacon QC and correction on EWAS results by Tikaaa2sahaaaq2c • 0
In the world of mobile games, the 88ef game download has gained traction for its performance driven design [free download][1], similar to …
Comment: using limma trend workflow in CAMERA by A.Barden ▴ 20
Do you need to set trend.var=TRUE when using camera in the limma-voom pipeline with RNA-Seq data (as apposed to limma-trend pipeline)?
Comment: Upcoming Ensembl API and data access changes - new blog post available by Tikaaa2sahaaaq2c • 0
Just as the Ensembl team transitions to a new platform for streamlined data access, diners can benefit from a digital newks menu prices con…
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Comment: using limma trend workflow in CAMERA
C: z-score with DESeq2?
Answer: What happens to genes with low dispersion during dispersion shrinkage in DESeq2
Comment: Are transformed values from rlog /vst log2 normalized counts?
Answer: Are transformed values from rlog /vst log2 normalized counts?
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