Showing : GAGE • reset
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593
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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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2.5k
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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0
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719
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.0 years ago OST • 0
0
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0
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743
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.1 years ago by 41k • written 2.1 years ago by • 0
6
votes
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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632
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Setting threshold with gage for gene set analysis
gage gageData
3.1 years ago jd348 • 0
1
vote
2
replies
1.2k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 3.3 years ago by ▴ 30
1
vote
1
reply
921
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Which group is meant by greater oder less in the gage results?
gage
updated 3.3 years ago by ★ 1.6k • written 3.4 years ago by ▴ 10
0
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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 11 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 3.7 years ago by ▴ 10
2
votes
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 4.0 years ago by 65k • written 4.0 years ago by • 0
0
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0
replies
874
views
gage function problem in R
gage R kegg pathview
updated 4.2 years ago by 41k • written 4.2 years ago by • 0
0
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0
replies
949
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
replies
1.2k
views
kegg.gsets: unknown species
gage
4.6 years ago mel.p • 0
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
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1
reply
1.4k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 11 months ago by • 0 • written 5.5 years ago by • 0
0
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0
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892
views
GAGE for non model organism
gage package gage
5.8 years ago melkile26 • 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 5.8 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
reply
1.3k
views
GAGE function and the same.dir option
gage gene set testing
updated 5.9 years ago by ★ 1.6k • written 5.9 years ago by ▴ 20
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
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
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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
replies
1.3k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.2 years ago Luo Weijun ★ 1.6k
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
1
vote
2
replies
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
replies
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 6.9 years ago by ★ 1.6k • written 7.0 years ago by • 0
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
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0
replies
1.1k
views
gage pca loadings
pca gage loadings
7.1 years ago MT ▴ 10
0
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0
replies
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
views
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
replies
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
votes
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 7.5 years ago by • 0
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
1
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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
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
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
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
13
replies
2.1k
views
Gage and setp argument
gsea gage
8.0 years ago • updated 7.9 years ago peter.chernek • 0
0
votes
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
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
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
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
8.4 years ago user31888 ▴ 30
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
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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
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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Answer: PCA plot suggestions by Michael Love 41k
For help with interpretation and design of analysis, I recommend working with a local statistician. Due to time restrictions, I can only…
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length by ussarizona ▴ 10
Hi Michael, Yes, I could figure it out what does the error mean. In my matrix I had the first colum GeneID while in my condition I only h…
Answer: Deseq2. decontXcounts not integers. Useful alternative? by Michael Love 41k
Another option would be to put the per sample estimated contamination in the design. This is for example how RUV etc help remove spurious D…
Answer: ATACseq merge peaks by ATpoint ★ 4.0k
That depends on your analysis. Typically, for differential analysis (and convenience) you would produce a single set of peaks (e.g. by merg…
Comment: Deseq2. decontXcounts not integers. Useful alternative? by camp ▴ 10
Yes, @atpoint is correct. decontX decontaminated counts are not integers due to the way the variation inference algorithm works, but you ca…
Votes
Comment: DESeq2 Error in `.rowNamesDF<-`(x, value = value): Invalid 'row.names' length
Comment: Deseq2. decontXcounts not integers. Useful alternative?
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
biomaRt error: database disk image is malformed
Comment: biomaRt : No lock file for BiocFileCache
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