Showing : gage • reset
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
12 weeks ago OST • 0
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123
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3 months ago by 37k • written 3 months ago by • 0
6
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5
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670
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KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 15 months ago by ★ 1.5k • written 15 months ago by • 0
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212
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Setting threshold with gage for gene set analysis
gage gageData
15 months ago jd348 • 0
1
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2
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490
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Can I create a gene set using GAGE?
gage pathview gageData
written 17 months ago by ▴ 30
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1
reply
312
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Which group is meant by greater oder less in the gage results?
gage
updated 18 months ago by ★ 1.5k • written 18 months ago by ▴ 10
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1
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385
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Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 20 months ago by 3.6k • written 20 months ago by • 0
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3
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520
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Creating gene set data for yeast
GAGE gene set go.gsets
updated 23 months ago by ★ 1.5k • written 23 months ago by ▴ 10
2
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3
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402
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Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 2.2 years ago by 60k • written 2.2 years ago by • 0
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0
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338
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gage function problem in R
gage R kegg pathview
updated 2.4 years ago by 37k • written 2.4 years ago by • 0
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446
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
2.7 years ago MimR • 0
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4
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614
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kegg.gsets: unknown species
gage
2.8 years ago mel.p • 0
3
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7
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2.2k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 2.9 years ago by ▴ 260 • written 2.9 years ago by ▴ 10
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694
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Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
3.7 years ago owen.donohoe • 0
1
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5
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1.8k
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KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 11 months ago by • 0 • written 3.9 years ago by ▴ 20
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509
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GAGE for non model organism
gage package gage
3.9 years ago melkile26 • 0
1
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2
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603
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
4.0 years ago atakanekiz ▴ 30
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1
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697
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GAGE function and the same.dir option
gage gene set testing
updated 4.1 years ago by ★ 1.5k • written 4.1 years ago by ▴ 20
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2
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2.2k
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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 4 months ago by • 0 • written 4.4 years ago by • 0
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3
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1.0k
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How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
4.4 years ago colaneri ▴ 30
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2
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902
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Error when installing package gageData
gage kegg
4.4 years ago colaneri ▴ 30
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709
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pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
4.4 years ago Luo Weijun ★ 1.5k
4
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5
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1.0k
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GAGE after tximport
gage tximport
updated 4.7 years ago by ★ 1.5k • written 4.7 years ago by ▴ 230
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3
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1.0k
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GAGE: No significant output while it should have
GAGE
updated 4.8 years ago by ★ 1.5k • written 4.9 years ago by ▴ 10
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2
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1.1k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 4.8 years ago by ★ 1.5k • written 4.8 years ago by • 0
2
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11
replies
2.8k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
5.0 years ago • updated 4.9 years ago Luo Weijun ★ 1.5k
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1
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739
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GAGE: no essential member genes for some DE pathways
gage
updated 5.1 years ago by ★ 1.5k • written 5.2 years ago by • 0
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1
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1.3k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 5.2 years ago by ★ 1.5k • written 5.2 years ago by • 0
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0
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755
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gage pca loadings
pca gage loadings
5.3 years ago MT ▴ 10
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739
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
5.4 years ago avinash gupta ▴ 130
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0
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871
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
5.4 years ago user31888 ▴ 30
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4
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1.3k
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Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
5.5 years ago bioinf ▴ 10
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2
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1.1k
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Questions about Pathview, maybe also gage
Pathview Gage R
updated 5.5 years ago by ▴ 10 • written 6.0 years ago by • 0
0
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2
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1.0k
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 5.5 years ago by ★ 1.5k • written 5.5 years ago by ▴ 30
1
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4
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1.5k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 5.6 years ago by ★ 1.2k • written 5.9 years ago by ▴ 100
0
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2
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943
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How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 5.7 years ago by ★ 1.5k • written 5.7 years ago by • 0
0
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4
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1.1k
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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 5.8 years ago by ▴ 40 • written 5.8 years ago by • 0
1
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3
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907
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DESeq2 rlog as input for GAGE
deseq2 gage
6.0 years ago Tom ▴ 10
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6
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1.6k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 6.0 years ago by ★ 1.5k • written 6.1 years ago by • 0
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13
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1.3k
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Gage and setp argument
gsea gage
6.2 years ago • updated 6.1 years ago peter.chernek • 0
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1
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842
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Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 6.4 years ago by ★ 1.5k • written 6.4 years ago by • 0
1
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3
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1.0k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
6.4 years ago serpalma.v ▴ 60
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2
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997
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 6.6 years ago by ★ 1.5k • written 6.6 years ago by ▴ 30
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1.7k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
6.6 years ago user31888 ▴ 30
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5
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2.1k
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GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 6.6 years ago by ★ 6.7k • written 6.6 years ago by ▴ 30
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4
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1.5k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
6.8 years ago martin.hoelzer ▴ 20
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832
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Detail of GAGE's esset.grp function
gage
6.9 years ago jackipchiho ▴ 10
2
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2
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1.2k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 7.0 years ago by ★ 1.5k • written 7.0 years ago by • 0
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0
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1.1k
views
How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
7.0 years ago jackipchiho ▴ 10
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9
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2.3k
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Urgent: Do GAGE applicable for non model species?
gage
updated 7.0 years ago by • 0 • written 7.0 years ago by ▴ 10
50 results • Page 1 of 1
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Comment: converting position from '-' strand to '+' strand by analeonpalacio ▴ 10
Hi Hervé, Thanks for the explanation. I am a bit confused about the conventions used by Ensembl. In some cases (insertions), the coordinate…
Comment: rename phenotypic variables in pData (microarray) or colData (RNA-Seq) by Basti ▴ 330
Could you share an example of your dataset( `dput(...)`) ? I tried with a random ExpressionSet and `names(p(Data(dataset))[1] <- "New_VAR"`…
Comment: rename phenotypic variables in pData (microarray) or colData (RNA-Seq) by jogugil • 0
names(pData(microarray))[1]<- "NEW_VAR" It doesn't work, it gives the following error: invalid (NULL) left side of assignment you canno…
Answer: Can't Install ensembldb and EnsDb.Hsapiens.v86 by elmfinds • 0
Thank you mbk0asis and Johannes! Installing png solved my issue. I appreciate your help!
Comment: Combine GRanges(List) to a single GRanges with unified breakpoints by Rodrigo • 0
Hi @malcolm-cook-6293 , Thanks again for the help. The code got me started albeit, I changed a bit the handling of the metadata. ``` #'…
Votes
how do singleton samples contribute to dispersion estimate in DESeq2?
Answer: Combine GRanges(List) to a single GRanges with unified breakpoints
Answer: Combine GRanges(List) to a single GRanges with unified breakpoints
Comment: RSEM - tximport; where is effective_length information used? Implications for sc
A: Appropriate explanation of the methodology behind arrayWeights function from lim
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