Showing : gage • reset
0
votes
0
replies
123
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
4 months ago OST • 0
0
votes
0
replies
152
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 5 months ago by 37k • written 5 months ago by • 0
6
votes
5
replies
721
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 17 months ago by ★ 1.5k • written 17 months ago by • 0
0
votes
0
replies
228
views
Setting threshold with gage for gene set analysis
gage gageData
17 months ago jd348 • 0
1
vote
2
replies
519
views
Can I create a gene set using GAGE?
gage pathview gageData
written 19 months ago by ▴ 30
1
vote
1
reply
339
views
Which group is meant by greater oder less in the gage results?
gage
updated 20 months ago by ★ 1.5k • written 20 months ago by ▴ 10
0
votes
1
reply
430
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 21 months ago by 3.6k • written 21 months ago by • 0
1
vote
3
replies
555
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 2.0 years ago by ★ 1.5k • written 2.1 years ago by ▴ 10
2
votes
3
replies
432
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 2.3 years ago by 60k • written 2.3 years ago by • 0
0
votes
0
replies
371
views
gage function problem in R
gage R kegg pathview
updated 2.5 years ago by 37k • written 2.5 years ago by • 0
0
votes
0
replies
471
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
2.8 years ago MimR • 0
0
votes
4
replies
655
views
kegg.gsets: unknown species
gage
2.9 years ago mel.p • 0
3
votes
7
replies
2.4k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 3.0 years ago by ▴ 260 • written 3.0 years ago by ▴ 10
0
votes
0
replies
731
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
3.8 years ago owen.donohoe • 0
1
vote
5
replies
1.9k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 13 months ago by • 0 • written 4.1 years ago by ▴ 20
0
votes
0
replies
535
views
GAGE for non model organism
gage package gage
4.1 years ago melkile26 • 0
1
vote
2
replies
627
views
GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
4.1 years ago atakanekiz ▴ 30
0
votes
1
reply
732
views
GAGE function and the same.dir option
gage gene set testing
updated 4.2 years ago by ★ 1.5k • written 4.2 years ago by ▴ 20
0
votes
2
replies
2.4k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 5 months ago by • 0 • written 4.5 years ago by • 0
0
votes
3
replies
1.1k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
4.5 years ago colaneri ▴ 30
0
votes
2
replies
948
views
Error when installing package gageData
gage kegg
4.5 years ago colaneri ▴ 30
0
votes
0
replies
731
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
4.5 years ago Luo Weijun ★ 1.5k
4
votes
5
replies
1.1k
views
GAGE after tximport
gage tximport
updated 4.8 years ago by ★ 1.5k • written 4.8 years ago by ▴ 230
0
votes
3
replies
1.0k
views
GAGE: No significant output while it should have
GAGE
updated 4.9 years ago by ★ 1.5k • written 5.0 years ago by ▴ 10
1
vote
2
replies
1.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 4.9 years ago by ★ 1.5k • written 4.9 years ago by • 0
2
votes
11
replies
2.9k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
5.1 years ago Luo Weijun ★ 1.5k
0
votes
1
reply
755
views
GAGE: no essential member genes for some DE pathways
gage
updated 5.3 years ago by ★ 1.5k • written 5.3 years ago by • 0
0
votes
1
reply
1.3k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 5.3 years ago by ★ 1.5k • written 5.3 years ago by • 0
0
votes
0
replies
770
views
gage pca loadings
pca gage loadings
5.4 years ago MT ▴ 10
0
votes
0
replies
753
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
5.5 years ago avinash gupta ▴ 130
0
votes
0
replies
893
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
5.5 years ago user31888 ▴ 30
0
votes
4
replies
1.3k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
5.6 years ago bioinf ▴ 10
0
votes
2
replies
1.1k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 5.6 years ago by ▴ 10 • written 6.1 years ago by • 0
0
votes
2
replies
1.0k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 5.7 years ago by ★ 1.5k • written 5.7 years ago by ▴ 30
1
vote
4
replies
1.5k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 5.8 years ago by ★ 1.2k • written 6.0 years ago by ▴ 100
0
votes
2
replies
968
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 5.8 years ago by ★ 1.5k • written 5.8 years ago by • 0
0
votes
4
replies
1.2k
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 5.9 years ago by ▴ 40 • written 5.9 years ago by • 0
1
vote
3
replies
930
views
DESeq2 rlog as input for GAGE
deseq2 gage
6.1 years ago Tom ▴ 10
0
votes
6
replies
1.7k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 6.1 years ago by ★ 1.5k • written 6.2 years ago by • 0
0
votes
13
replies
1.3k
views
Gage and setp argument
gsea gage
6.3 years ago peter.chernek • 0
0
votes
1
reply
860
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 6.5 years ago by ★ 1.5k • written 6.5 years ago by • 0
1
vote
3
replies
1.0k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
6.5 years ago serpalma.v ▴ 60
0
votes
2
replies
1.0k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 6.7 years ago by ★ 1.5k • written 6.7 years ago by ▴ 30
0
votes
0
replies
1.7k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
6.7 years ago user31888 ▴ 30
2
votes
5
replies
2.2k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 6.7 years ago by ★ 6.7k • written 6.8 years ago by ▴ 30
0
votes
4
replies
1.5k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
6.9 years ago martin.hoelzer ▴ 20
0
votes
0
replies
848
views
Detail of GAGE's esset.grp function
gage
7.0 years ago jackipchiho ▴ 10
2
votes
2
replies
1.2k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 7.1 years ago by ★ 1.5k • written 7.1 years ago by • 0
0
votes
0
replies
1.1k
views
How to fully use the list of DEGs in non model species?
deseq2 gage ebseq rnaseq
7.1 years ago jackipchiho ▴ 10
0
votes
9
replies
2.4k
views
Urgent: Do GAGE applicable for non model species?
gage
updated 7.1 years ago by • 0 • written 7.1 years ago by ▴ 10
50 results • Page 1 of 1
Recent ...
Replies
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
It's relevant for me, thank you for the information!
Comment: An ESR essay about software design, and how it applies to Bioconductor by Gary • 0
Thank you for sharing!
Comment: conditional command within GRanges by Basti ▴ 390
I can't reproduce your issue because you did not provided an example of your dataset (example with `dput(head(data1))`, but in the first ca…
Comment: Error in Create switchAnalyzeRlist by k.vitting.seerup ▴ 120
That sounds like you have the wrong version of the annotation compared to which version you used for the quantification?
Comment: Error in Create switchAnalyzeRlist by bpshtiwan ▴ 10
Great... now it is same. but still I have problem with four possibilities during using IsoformSwitchAnalyzeR. Knidly, any idea where is the…
Votes
A: EGSEA error during report generation: "only 0's may be mixed with negative subsc
Answer: mapToAlignments_issue
Analysis of peaks generated from Homer using Diffbind
How to select summit size for histone ChiP-Seq in Diffbind
Comment: GSEA with Wikipathways not entirely reproducible
Awards • All
Popular Question to e.iich • 0
Popular Question to Gordon Smyth 46k
Popular Question to gv ▴ 40
Scholar to Hervé Pagès 15k
Popular Question to ta_awwad ▴ 10
Locations • All
Switzerland, just now
United States, just now
Germany, 5 minutes ago
Norway, 6 minutes ago
United States, 7 minutes ago
Traffic: 424 users visited in the last hour
Content Search
Users
Tags
Badges
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6