Showing : gage • reset
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
5 months ago cereyredondo • 0
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0
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250
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
7 months ago danalvoronov ▴ 10
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1
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829
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what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 21 months ago by 67k • written 21 months ago by ▴ 10
3
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13
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3.1k
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pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
2.3 years ago • updated 22 months ago nute11a ▴ 10
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985
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
2.7 years ago OST • 0
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0
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951
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 2.8 years ago by 43k • written 2.8 years ago by • 0
6
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5
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1.8k
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KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 3.8 years ago by ★ 1.6k • written 3.8 years ago by • 0
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0
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787
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Setting threshold with gage for gene set analysis
gage gageData
3.8 years ago jd348 • 0
1
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2
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1.4k
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Can I create a gene set using GAGE?
gage pathview gageData
written 3.9 years ago by ▴ 40
1
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1
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1.1k
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Which group is meant by greater oder less in the gage results?
gage
updated 4.0 years ago by ★ 1.6k • written 4.0 years ago by ▴ 20
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2
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1.5k
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Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 19 months ago by • 0 • written 4.1 years ago by • 0
1
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3
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1.5k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 4.4 years ago by ★ 1.6k • written 4.4 years ago by ▴ 10
2
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3
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1.7k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 4.7 years ago by 67k • written 4.7 years ago by • 0
0
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0
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1.1k
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gage function problem in R
gage R kegg pathview
updated 4.9 years ago by 43k • written 4.9 years ago by • 0
0
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0
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1.2k
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KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
5.2 years ago MimR • 0
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4
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1.5k
views
kegg.gsets: unknown species
gage
5.2 years ago mel.p • 0
5
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7
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9.6k
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Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 5.3 years ago by ▴ 280 • written 5.3 years ago by ▴ 10
0
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1
reply
1.6k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 19 months ago by • 0 • written 6.2 years ago by • 0
1
vote
5
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3.3k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 3.4 years ago by • 0 • written 6.4 years ago by ▴ 40
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0
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1.0k
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GAGE for non model organism
gage package gage
6.4 years ago melkile26 • 0
1
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2
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1.4k
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GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
6.4 years ago atakanekiz ▴ 30
0
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1
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1.5k
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GAGE function and the same.dir option
gage gene set testing
updated 6.6 years ago by ★ 1.6k • written 6.6 years ago by ▴ 20
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2
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4.0k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 2.8 years ago by • 0 • written 6.8 years ago by • 0
0
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3
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2.2k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
6.8 years ago colaneri ▴ 30
0
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2
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1.8k
views
Error when installing package gageData
gage kegg
6.9 years ago colaneri ▴ 30
0
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0
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1.4k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
6.9 years ago Luo Weijun ★ 1.6k
4
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5
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2.0k
views
GAGE after tximport
gage tximport
updated 7.1 years ago by ★ 1.6k • written 7.1 years ago by ▴ 230
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3
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1.8k
views
GAGE: No significant output while it should have
GAGE
updated 7.2 years ago by ★ 1.6k • written 7.3 years ago by ▴ 10
1
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2
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2.5k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 7.2 years ago by ★ 1.6k • written 7.2 years ago by • 0
2
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11
replies
5.2k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
7.4 years ago Luo Weijun ★ 1.6k
0
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1
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1.3k
views
GAGE: no essential member genes for some DE pathways
gage
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
0
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1
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2.1k
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GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 7.6 years ago by ★ 1.6k • written 7.6 years ago by • 0
0
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0
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1.3k
views
gage pca loadings
pca gage loadings
7.7 years ago MT ▴ 10
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1.4k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
7.8 years ago avinash gupta ▴ 130
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0
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1.5k
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GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
7.8 years ago user31888 ▴ 30
0
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4
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2.3k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.0 years ago bioinf ▴ 10
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2
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1.9k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 8.0 years ago by ▴ 10 • written 8.5 years ago by • 0
0
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2
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1.8k
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 30
1
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4
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2.6k
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GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 8.1 years ago by ★ 1.2k • written 8.3 years ago by ▴ 110
0
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2
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1.8k
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How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 8.1 years ago by ★ 1.6k • written 8.2 years ago by • 0
0
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4
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2.2k
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 8.2 years ago by ▴ 40 • written 8.2 years ago by • 0
1
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3
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1.7k
views
DESeq2 rlog as input for GAGE
deseq2 gage
8.4 years ago Tom ▴ 10
0
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6
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4.2k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 8.5 years ago by ★ 1.6k • written 8.6 years ago by • 0
0
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13
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2.5k
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Gage and setp argument
gsea gage
8.6 years ago peter.chernek • 0
0
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1
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1.4k
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 8.8 years ago by ★ 1.6k • written 8.8 years ago by • 0
1
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3
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1.8k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
8.8 years ago serpalma.v ▴ 60
0
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2
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1.7k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 9.0 years ago by ★ 1.6k • written 9.0 years ago by ▴ 30
0
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0
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2.4k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
9.1 years ago user31888 ▴ 30
2
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5
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3.2k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.1 years ago by ★ 6.8k • written 9.1 years ago by ▴ 30
0
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4
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2.6k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
9.3 years ago • updated 9.2 years ago martin.hoelzer ▴ 20
50 results • Page 1 of 1
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Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Robert Castelo ★ 3.4k
Hi Hervé, thank you very much for your input into how to properly build and manage TxDb objects. gDNAx has two main inputs, one or more BAM…
Comment: Biostrings: Error writing long reads (>200 kbps) with writeQualityScaledXStringS by Aidan ▴ 60
Quick update: this is fixed in a branch awaiting PR to Biostrings (https://github.com/Bioconductor/Biostrings/pull/122). Should be in `deve…
Answer: Can DESeq2's design compensate for sequencing experimental design shortcomings? by Michael Love 43k
For statistical analysis plans, I recommend working with a local statistician or someone familiar with linear models in R. I have to reserv…
Comment: how should I apply "cpg.annotate" to TCGA methylation data in hg38 for HM450K? by xiaofeiwang198266 • 0
Thanks for your reply!
Comment: Issues with seqlevelsStyle when making custom txdb objects for genomes/annotatio by Hervé Pagès 16k
> I have requested gDNAx developers for a feature request to turn off seqlevelsStyle(txdb) Yes, that's the right course of action. `seqlev…
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C: edgeR and lack of counts ID on CPM matrix
A: DESeq2 Following RSEM
A: importing RSEM data into DESeq2
A: Expected counts from RSEM in DESeq2
A: Using RSEM reads for DESeq2
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