Showing : gage • reset
0
votes
1
reply
133
views
what does "exp1" mean in the gage() function?
gage clusterProfiler DESeq2
updated 10 weeks ago by 63k • written 10 weeks ago by ▴ 10
0
votes
13
replies
1.2k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST KEGG gage pathview
9 months ago • updated 4 months ago nute11a • 0
0
votes
0
replies
356
views
Pathway Analysis using GAGE
gage RNASeq gageData Pathways
14 months ago OST • 0
0
votes
0
replies
416
views
Gage pathway analysis of RNAseq graphical representation as dot plot
gage plot RNASeq goseq
updated 15 months ago by 40k • written 15 months ago by • 0
6
votes
5
replies
1.0k
views
KEGG analysis for plasmodium
KEGG gage gageData pathview
updated 2.2 years ago by ★ 1.6k • written 2.2 years ago by • 0
0
votes
0
replies
385
views
Setting threshold with gage for gene set analysis
gage gageData
2.2 years ago jd348 • 0
1
vote
2
replies
798
views
Can I create a gene set using GAGE?
gage pathview gageData
written 2.4 years ago by ▴ 30
1
vote
1
reply
565
views
Which group is meant by greater oder less in the gage results?
gage
updated 2.5 years ago by ★ 1.6k • written 2.5 years ago by ▴ 10
0
votes
2
replies
777
views
Pathway analysis using GAGE returns all NA values
gage rna-seq pathwayanalysis
updated 27 days ago by • 0 • written 2.6 years ago by • 0
1
vote
3
replies
776
views
Creating gene set data for yeast
GAGE gene set go.gsets
updated 2.8 years ago by ★ 1.6k • written 2.9 years ago by ▴ 10
2
votes
3
replies
739
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw R gage
updated 3.1 years ago by 63k • written 3.1 years ago by • 0
0
votes
0
replies
554
views
gage function problem in R
gage R kegg pathview
updated 3.4 years ago by 40k • written 3.4 years ago by • 0
0
votes
0
replies
692
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage pathview KEGG Gene enrichment analysis
3.6 years ago MimR • 0
0
votes
4
replies
875
views
kegg.gsets: unknown species
gage
3.7 years ago mel.p • 0
4
votes
7
replies
4.5k
views
Comparison between two different group's pathway analysis results
gage DESeq2 pathway analysis
updated 3.8 years ago by ▴ 270 • written 3.8 years ago by ▴ 10
0
votes
1
reply
1.0k
views
Keep getting NaN Values in GAGE analysis of KEGG pathways
KEGG GAGE NaN R DESeq2
updated 27 days ago by • 0 • written 4.6 years ago by • 0
1
vote
5
replies
2.4k
views
KEGG enrichment for non-model
kegg pathway analysis non-model gage pathview
updated 22 months ago by • 0 • written 4.9 years ago by ▴ 20
0
votes
0
replies
679
views
GAGE for non model organism
gage package gage
4.9 years ago melkile26 • 0
1
vote
2
replies
835
views
GAGE analysis with the whole or a subset of matrix
gage gage package gene expression matrix gene set analysis
4.9 years ago atakanekiz ▴ 30
0
votes
1
reply
951
views
GAGE function and the same.dir option
gage gene set testing
updated 5.0 years ago by ★ 1.6k • written 5.0 years ago by ▴ 20
0
votes
2
replies
3.1k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage gage package pathview rna-seq
updated 15 months ago by • 0 • written 5.3 years ago by • 0
0
votes
3
replies
1.4k
views
How to produce a dataframe with unique ENTREZID to use in gage?
gage annotationdbi entrez ensembl
5.3 years ago colaneri ▴ 30
0
votes
2
replies
1.2k
views
Error when installing package gageData
gage kegg
5.3 years ago colaneri ▴ 30
0
votes
0
replies
945
views
pathview and gage server connection issue
pathview gage pathway analysis kegg visualization
5.3 years ago Luo Weijun ★ 1.6k
4
votes
5
replies
1.3k
views
GAGE after tximport
gage tximport
updated 5.6 years ago by ★ 1.6k • written 5.6 years ago by ▴ 230
0
votes
3
replies
1.2k
views
GAGE: No significant output while it should have
GAGE
updated 5.7 years ago by ★ 1.6k • written 5.8 years ago by ▴ 10
1
vote
2
replies
1.6k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE Gene Ontology rna-seq pathview
updated 5.7 years ago by ★ 1.6k • written 5.7 years ago by • 0
2
votes
11
replies
3.5k
views
Recent build and parsing error in pathview
pathview KEGGgraph gage pathway pathway analysis
5.9 years ago Luo Weijun ★ 1.6k
0
votes
1
reply
898
views
GAGE: no essential member genes for some DE pathways
gage
updated 6.1 years ago by ★ 1.6k • written 6.1 years ago by • 0
0
votes
1
reply
1.5k
views
GAGE or GSEABase using expression data and pathway.gmt file for mouse
R GSEA GAGE pathways
updated 6.1 years ago by ★ 1.6k • written 6.1 years ago by • 0
0
votes
0
replies
908
views
gage pca loadings
pca gage loadings
6.2 years ago MT ▴ 10
0
votes
0
replies
903
views
Pathway analysis for diffrential express gene
pathways gage annotation gostats
6.3 years ago avinash gupta ▴ 130
0
votes
0
replies
1.1k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage deseq pathview
6.3 years ago user31888 ▴ 30
0
votes
4
replies
1.6k
views
Error: Pathway analysis using Sleuth results
pathview gage rna-seq R sleuth
6.4 years ago bioinf ▴ 10
0
votes
2
replies
1.3k
views
Questions about Pathview, maybe also gage
Pathview Gage R
updated 6.4 years ago by ▴ 10 • written 6.9 years ago by • 0
0
votes
2
replies
1.2k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE pathview
updated 6.5 years ago by ★ 1.6k • written 6.5 years ago by ▴ 30
1
vote
4
replies
1.8k
views
GO slim data for GAGE GSEA analysis
GSEA GAGE GO
updated 6.6 years ago by ★ 1.2k • written 6.8 years ago by ▴ 110
0
votes
2
replies
1.2k
views
How to extract essential genes from pathway (essGene) using DEseq2/GAGE workflow?
gage gage package
updated 6.6 years ago by ★ 1.6k • written 6.7 years ago by • 0
0
votes
4
replies
1.4k
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 6.7 years ago by ▴ 40 • written 6.7 years ago by • 0
1
vote
3
replies
1.2k
views
DESeq2 rlog as input for GAGE
deseq2 gage
6.9 years ago Tom ▴ 10
0
votes
6
replies
2.4k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage pathview error
updated 7.0 years ago by ★ 1.6k • written 7.0 years ago by • 0
0
votes
13
replies
1.7k
views
Gage and setp argument
gsea gage
7.1 years ago peter.chernek • 0
0
votes
1
reply
976
views
Using Gage and pathview with previously processed data
pathview gage r kegg rnaseq
updated 7.3 years ago by ★ 1.6k • written 7.3 years ago by • 0
1
vote
3
replies
1.2k
views
Discrepancy in gene set size between gage() and geneData()
gage gene set analysis pathview kegg pathway analysis
7.3 years ago serpalma.v ▴ 60
0
votes
2
replies
1.2k
views
GAGE from Cuffdiff workflow: Error in names(cuff.fc) = gnames : attempt to set an attribute on NULL
GAGE Cuffdiff gene names
updated 7.5 years ago by ★ 1.6k • written 7.5 years ago by ▴ 30
0
votes
0
replies
1.9k
views
Cannot install GAGE (and its dependencies): libpng16.so.16 not found
GAGE libpn
7.5 years ago user31888 ▴ 30
2
votes
5
replies
2.5k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps GAGE
updated 7.6 years ago by ★ 6.8k • written 7.6 years ago by ▴ 30
0
votes
4
replies
1.8k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage pathview
7.7 years ago martin.hoelzer ▴ 20
0
votes
0
replies
974
views
Detail of GAGE's esset.grp function
gage
7.8 years ago jackipchiho ▴ 10
2
votes
2
replies
1.4k
views
Output from pathview does not seem to match input
pathview gage pathway analysis
updated 7.9 years ago by ★ 1.6k • written 7.9 years ago by • 0
50 results • Page 1 of 1
Recent ...
Replies
Answer: multiple filters in biomaRt by RuBBiT0 ▴ 10
First, yes, one gene could be related to several GO ID, and the result is based on the annotation package you use. Second, could you pro…
Comment: Diffbind "No genome detected" by kyliecode • 0
Hi Dr. Stark, Thanks very much for your reply! The bam files were output from nf-core/chipseq pipeline and for some reason, they do not ha…
Answer: Discrepancy between DESeq2 files produced in Galaxy and R(RStudio) by Michael Love 40k
I guess that Galaxy may be using some kind of LFC shrinkage, but without seeing their code I wouldn't know for sure. Shrinkage generally…
Comment: TCGAbiolinks cannot find bcr_patient_barcode by Habil Zare ▴ 170
I checked your example with the devel version 2.29.6 on Bioc and it worked fine. Thanks for the fix!
Answer: error in ChAMP loading file by jenniferbrowngates • 0
I got a lot of information from this website about different topics which is beneficial for me too so I thank this site and also suggest a …
Votes
Answer: Using PEER to identify hidden confounders in RNA-seq data (not working)
Comment: Error: biomaRt has encountered an unexpected server error.
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Comment: Interpret plot from DiffBind
Awards • All
Scholar to Tiago C. Silva ▴ 270
Popular Question to reba.duncan • 0
Popular Question to tntntntntn ▴ 10
Popular Question to rodrigo.duarte88 ▴ 30
Scholar to Rory Stark ★ 4.9k
Locations • All
Peru, 2 minutes ago
WEHI, Melbourne, Australia, 18 minutes ago
United States, 20 minutes ago
United States, 49 minutes ago
United States, 1 hour ago
Traffic: 326 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