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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2.5k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
20 months ago • updated 14 months ago nute11a ▴ 10
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0
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716
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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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740
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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
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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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630
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Setting threshold with gage for gene set analysis
gage gageData
3.1 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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919
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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
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2
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1.2k
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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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1.1k
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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
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3
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1.3k
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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
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871
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
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946
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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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1.2k
views
kegg.gsets: unknown species
gage
4.6 years ago mel.p • 0
4
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7
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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
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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 11 months ago by • 0 • written 5.5 years ago by • 0
0
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0
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890
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GAGE for non model organism
gage package gage
5.8 years ago melkile26 • 0
1
vote
5
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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
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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
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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
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2
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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
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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
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2
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2.1k
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
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3
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1.5k
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
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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
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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
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gage pca loadings
pca gage loadings
7.1 years ago MT ▴ 10
0
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0
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1.2k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.2 years ago avinash gupta ▴ 130
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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
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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 7.5 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 7.4 years ago by ★ 1.2k • written 7.7 years ago by ▴ 110
1
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3
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1.5k
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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
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Questions about Pathview, maybe also gage
Pathview Gage R
updated 7.3 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 7.8 years ago by ★ 1.6k • written 7.9 years ago by • 0
0
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13
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2.1k
views
Gage and setp argument
gsea gage
8.0 years ago • updated 7.9 years ago peter.chernek • 0
0
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1
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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
8.4 years ago user31888 ▴ 30
2
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5
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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
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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
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Detail of GAGE's esset.grp function
gage
8.7 years ago jackipchiho ▴ 10
2
votes
2
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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
Recent ...
Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you for your answer and precise exemple ! It is disappointing but makes sense. Best, Alexandre
Comment: How to retrieve gene ontology GO class from gene list? by James W. MacDonald 65k
Yes. The `keys` argument to both `select` and `mapIds` will accept a vector (see `?select` for more information). Also, the [vignette][1] f…
Comment: How to retrieve gene ontology GO class from gene list? by bandconductor • 0
Thanks, this is potentially a much faster way than parsing BiomRt. However, it is only returning one GO term right now (biomaRt returns a f…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by James W. MacDonald 65k
Both `RUVseq` and `sva` are meant to be used to remove technical variability. The problem is the identification of variability that is tech…
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2 by Alexandre • 0
Hello James, Thank you very much for your answer and taking the time to read my post. I understand your remark, but isn't the approach o…
Votes
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
Answer: Use of negative binomial model for exponential decay rate estimation using DESeq
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
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