Showing : gage • reset
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441
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GAGE kegg.gsets() self-signed certificate error
gageData gage
7 months ago Lucas • 0
0
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0
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542
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How to use GAGE with my own metagenomic KOFams data
kegg.gsets gageData gage KEGG
15 months ago cereyredondo • 0
0
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0
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464
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GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO KEGG gage pathview
17 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 2.6 years ago by 68k • written 2.6 years ago by ▴ 10
3
votes
13
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4.0k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
3.2 years ago • updated 2.7 years ago nute11a ▴ 10
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0
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1.2k
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Pathway Analysis using GAGE
gage RNASeq gageData Pathways
3.5 years ago OST • 0
0
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0
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1.2k
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Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 3.6 years ago by 43k • written 3.6 years ago by • 0
6
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5
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2.3k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 4.6 years ago by ★ 1.6k • written 4.6 years ago by • 0
0
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0
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911
views
Setting threshold with gage for gene set analysis
gage gageData
4.6 years ago jd348 • 0
1
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2
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1.6k
views
Can I create a gene set using GAGE?
gage pathview gageData
written 4.8 years ago by ▴ 40
1
vote
1
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1.3k
views
Which group is meant by greater oder less in the gage results?
gage
updated 4.8 years ago by ★ 1.6k • written 4.9 years ago by ▴ 20
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2
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1.7k
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 2.5 years ago by • 0 • written 5.0 years ago by • 0
1
vote
3
replies
1.8k
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 5.2 years ago by ★ 1.6k • written 5.2 years ago by ▴ 10
2
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3
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2.2k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 5.5 years ago by 68k • written 5.5 years ago by • 0
0
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0
replies
1.3k
views
gage function problem in R
gage R kegg pathview
updated 5.7 years ago by 43k • written 5.7 years ago by • 0
0
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0
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1.5k
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
6.0 years ago MimR • 0
0
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4
replies
1.8k
views
kegg.gsets: unknown species
gage
6.1 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 6.2 years ago by ▴ 280 • written 6.2 years ago by ▴ 10
0
votes
1
reply
1.8k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 2.5 years ago by • 0 • written 7.0 years ago by • 0
1
vote
5
replies
3.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 4.3 years ago by • 0 • written 7.3 years ago by ▴ 40
0
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0
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1.2k
views
GAGE for non model organism
gage package gage
7.3 years ago melkile26 • 0
1
vote
2
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1.6k
views
GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
7.3 years ago atakanekiz ▴ 30
0
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1
reply
1.7k
views
GAGE function and the same.dir option
gage gene set testing
updated 7.4 years ago by ★ 1.6k • written 7.4 years ago by ▴ 20
0
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2
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4.5k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 3.6 years ago by • 0 • written 7.7 years ago by • 0
0
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3
replies
2.5k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
7.7 years ago colaneri ▴ 30
0
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2
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2.1k
views
Error when installing package gageData
gage kegg
7.7 years ago colaneri ▴ 30
0
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0
replies
1.6k
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
7.7 years ago Luo Weijun ★ 1.6k
4
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5
replies
2.3k
views
GAGE after tximport
gage tximport
updated 8.0 years ago by ★ 1.6k • written 8.0 years ago by ▴ 230
0
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3
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2.1k
views
GAGE: No significant output while it should have
GAGE
updated 8.1 years ago by ★ 1.6k • written 8.2 years ago by ▴ 10
1
vote
2
replies
3.0k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 8.1 years ago by ★ 1.6k • written 8.1 years ago by • 0
2
votes
11
replies
5.9k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
8.3 years ago Luo Weijun ★ 1.6k
0
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1
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1.5k
views
GAGE: no essential member genes for some DE pathways
gage
updated 8.4 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
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1
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2.4k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 8.5 years ago by ★ 1.6k • written 8.5 years ago by • 0
0
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0
replies
1.4k
views
gage pca loadings
pca gage loadings
8.6 years ago MT ▴ 10
0
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0
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1.6k
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Pathway analysis for diffrential express gene
pathways gage annotation gostats
8.7 years ago avinash gupta ▴ 130
0
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0
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1.6k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
8.7 years ago user31888 ▴ 30
0
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4
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2.6k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
8.8 years ago bioinf ▴ 10
0
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2
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2.2k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 8.8 years ago by ▴ 10 • written 9.3 years ago by • 0
0
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2
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2.0k
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GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 8.8 years ago by ★ 1.6k • written 8.9 years ago by ▴ 30
1
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4
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3.0k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 8.9 years ago by ★ 1.2k • written 9.2 years ago by ▴ 110
0
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2
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2.1k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 9.0 years ago by ★ 1.6k • written 9.0 years ago by • 0
0
votes
4
replies
2.5k
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 9.1 years ago by ▴ 40 • written 9.1 years ago by • 0
1
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3
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1.9k
views
DESeq2 rlog as input for GAGE
deseq2 gage
9.3 years ago Tom ▴ 10
0
votes
6
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4.8k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 9.3 years ago by ★ 1.6k • written 9.4 years ago by • 0
0
votes
13
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3.0k
views
Gage and setp argument
gsea gage
9.5 years ago • updated 9.4 years ago peter.chernek • 0
0
votes
1
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1.5k
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 9.7 years ago by ★ 1.6k • written 9.7 years ago by • 0
1
vote
3
replies
2.2k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
9.7 years ago serpalma.v ▴ 60
0
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2
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1.9k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 9.9 years ago by ★ 1.6k • written 9.9 years ago by ▴ 30
0
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0
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2.6k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
9.9 years ago user31888 ▴ 30
2
votes
5
replies
3.6k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 9.9 years ago by ★ 6.8k • written 9.9 years ago by ▴ 30
114 results • Page 1 of 3
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Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Aaron already answered your question. If you have an HDF5 file, it will be read in as a `TENxMatrix` object, which isn't actually read in -…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by dan.gatti • 0
Very strange. We have the same package versions. I tried adding the mtx.class, type, and delayed arguments, but it's still making the coun…
Comment: DESeq2 for candidate gene analysis by piffelpaff ▴ 20
thank you so much for answering Dr. Love!
Answer: DESeq2 for candidate gene analysis by Michael Love 43k
Your plan 1 is reasonable. Run DESeq2 on the whole dataset to obtain size factors and moderated dispersion estimates and then extract the u…
Comment: Best practice for handling large data (matrix with >2^31-1 non-zero elements) in by James W. MacDonald 68k
Oh. ``` > z <- read10xCounts(c(tmpdir, tmpdir), mtx.class = "SVT_SparseMatrix", delayed = TRUE) > class(counts(z)) [1] "DelayedMatrix" att…
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A: Multi-level experiments in Limma
Answer: Should voomWithQualityWeights still be used when the sample-specific weights var
Answer: DESeq2 for candidate gene analysis
DESeq2 for candidate gene analysis
Answer: DESeq2 for candidate gene analysis
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