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GAGE
•
reset
6
votes
5
replies
1.5k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.1 years ago by
Luo Weijun
★ 1.6k • written 3.1 years ago by
MOHAMMAD
• 0
4
votes
7
replies
7.2k
views
Comparison between two different group's pathway analysis results
gage
DESeq2
pathway analysis
updated 4.7 years ago by
mikhael.manurung
▴ 270 • written 4.7 years ago by
tntntntntn
▴ 10
4
votes
4
replies
7.8k
views
Packages for GO and KEGG analysis on RNAseq data
GO
gage
goseq
KEGG
updated 9.5 years ago by
Gordon Smyth
50k • written 9.6 years ago by
Merienne Nicolas
▴ 120
4
votes
5
replies
1.7k
views
GAGE after tximport
gage
tximport
updated 6.5 years ago by
Luo Weijun
★ 1.6k • written 6.5 years ago by
Ed Siefker
▴ 230
3
votes
13
replies
2.5k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
20 months ago • updated 14 months ago
nute11a
▴ 10
2
votes
3
replies
1.3k
views
Why pathview plot shows both colors(red and green) in up-regulated pathways?
pathveiw
R
gage
updated 4.0 years ago by
James W. MacDonald
65k • written 4.0 years ago by
nhwoo
• 0
2
votes
2
replies
1.7k
views
Output from pathview does not seem to match input
pathview
gage
pathway analysis
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
bdp
• 0
2
votes
11
replies
4.5k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
6.8 years ago
Luo Weijun
★ 1.6k
2
votes
5
replies
2.9k
views
GAGE pathway analysis (R/Bioconductor): summarizeOverlaps error
summarizeoverlaps
GAGE
updated 8.4 years ago by
Valerie Obenchain
★ 6.8k • written 8.4 years ago by
user31888
▴ 30
1
vote
5
replies
2.9k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 2.8 years ago by
najib
• 0 • written 5.8 years ago by
bekah
▴ 40
1
vote
1
reply
919
views
Which group is meant by greater oder less in the gage results?
gage
updated 3.3 years ago by
Luo Weijun
★ 1.6k • written 3.4 years ago by
Matthias Munz
▴ 10
1
vote
2
replies
1.2k
views
Can I create a gene set using GAGE?
gage
pathview
gageData
written 3.3 years ago by
Emilia
▴ 30
1
vote
2
replies
1.1k
views
GAGE analysis with the whole or a subset of matrix
gage
gage package
gene expression matrix
gene set analysis
5.8 years ago
atakanekiz
▴ 30
1
vote
3
replies
1.5k
views
DESeq2 rlog as input for GAGE
deseq2
gage
7.8 years ago
Tom
▴ 10
1
vote
3
replies
1.6k
views
Discrepancy in gene set size between gage() and geneData()
gage
gene set analysis
pathview
kegg
pathway analysis
8.2 years ago
serpalma.v
▴ 60
1
vote
4
replies
2.3k
views
GO slim data for GAGE GSEA analysis
GSEA
GAGE
GO
updated 7.4 years ago by
Guangchuang Yu
★ 1.2k • written 7.7 years ago by
rubi
▴ 110
1
vote
2
replies
2.1k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE
Gene Ontology
rna-seq
pathview
updated 6.6 years ago by
Luo Weijun
★ 1.6k • written 6.6 years ago by
JMallory
• 0
1
vote
0
replies
1.7k
views
Pathview and GAGE now work with essentially all KEGG species
Visualization
gage
pathview
Visualization
gage
pathview
10.5 years ago
Luo Weijun
★ 1.6k
1
vote
3
replies
1.1k
views
Creating gene set data for yeast
GAGE
gene set
go.gsets
updated 3.7 years ago by
Luo Weijun
★ 1.6k • written 3.7 years ago by
June.
▴ 10
0
votes
1
reply
1.5k
views
GAGE vs other GO analysis tools
Microarray
Pathways
GO
gage
Microarray
Pathways
GO
gage
updated 12.3 years ago by
Luo Weijun
★ 1.6k • written 12.3 years ago by
January Weiner
▴ 240
0
votes
3
replies
2.3k
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
Microarray
GO
Cancer
Breast
gage
Microarray
GO
Cancer
Breast
gage
updated 12.3 years ago by
Javerjung Sandhu
▴ 200 • written 12.3 years ago by
Valerie Obenchain
★ 6.8k
0
votes
0
replies
794
views
equiry about GAGE
Sequencing
gage
Sequencing
gage
13.4 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
898
views
gage
gage
gage
12.0 years ago
Luo Weijun
★ 1.6k
0
votes
2
replies
948
views
How to prepare Custom INPUT(DATA) files for GAGE Analysis and DO a BASIC GAGE analysis using those files
gage
gage
12.3 years ago
Javerjung Sandhu
▴ 200
0
votes
1
reply
1.1k
views
A error in GAGE analysis
gage
gage
updated 12.0 years ago by
Luo Weijun
★ 1.6k • written 12.0 years ago by
Javerjung Sandhu
▴ 200
0
votes
0
replies
1.1k
views
GAGE: script
GO
gage
GO
gage
11.5 years ago
Guest User
★ 13k
0
votes
2
replies
982
views
A question about the gage package
Microarray
probe
gage
Microarray
probe
gage
11.1 years ago
He, Yiwen NIH/CIT
▴ 360
0
votes
0
replies
899
views
A question about the gage package
Microarray
probe
gage
Microarray
probe
gage
11.1 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
793
views
sigGeneSet gage function
gage
gage
11.0 years ago
Vincenzo Capece
▴ 140
0
votes
0
replies
3.2k
views
Pathview+GAGE workflow on RNA-seq data pathway analysis and visualization (was: Pathview published in Bioinformatics)
Annotation
Pathways
Visualization
graph
PROcess
gage
pathview
Annotation
Pathways
graph
10.8 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.0k
views
GAGE heatmap pdf question...
GO
gage
GO
gage
12.1 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.3k
views
GAGE package help required
Pathways
gage
Pathways
gage
12.7 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.1k
views
gage package: biological replicates and technical replicates
gage
gage
updated 13.4 years ago by
Luo Weijun
★ 1.6k • written 13.4 years ago by
heyi xiao
▴ 360
0
votes
2
replies
1.7k
views
Questions about Pathview, maybe also gage
Pathview
Gage
R
updated 7.3 years ago by
bioinf
▴ 10 • written 7.8 years ago by
ChIP-Tease
• 0
0
votes
0
replies
849
views
GAGE heatmap pdf question...
GO
gage
GO
gage
12.2 years ago
Alan Derr
▴ 50
0
votes
1
reply
1.1k
views
GAGE Package: Problem with probeset IDs conversion to Gene names or vice versa
convert
gage
convert
gage
updated 12.1 years ago by
Luo Weijun
★ 1.6k • written 12.2 years ago by
Javerjung Sandhu
▴ 200
0
votes
0
replies
889
views
Biological replicates with Gage
gage
gage
12.7 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.0k
views
Redundant gene sets & gagePipe
gage
gage
10.4 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.1k
views
GAGE Package: Problem with "Affymetrix hg u133 plus 2 probeset IDs" conversion to Gene names or vice versa
convert
gage
convert
gage
12.2 years ago
Javerjung Sandhu
▴ 200
0
votes
0
replies
651
views
Redundant gene sets & gagePipe
gage
gage
10.4 years ago
Christian De Santis
▴ 150
0
votes
1
reply
1.3k
views
gage function---kegg.gsets
gage
gage
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
Guest User
★ 13k
0
votes
1
reply
1.5k
views
Can gage not use large gene sets for pathway analysis?
Pathways
gage
pathview
Pathways
gage
pathview
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
Guest User
★ 13k
0
votes
5
replies
2.3k
views
Rgraphviz installation issue
Rgraphviz
gage
Rgraphviz
gage
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
km
▴ 100
0
votes
1
reply
1.1k
views
GAGE analysis
Microarray
gage
Microarray
gage
updated 10.3 years ago by
Luo Weijun
★ 1.6k • written 10.3 years ago by
Roopa Subbaiaih
▴ 130
0
votes
1
reply
2.4k
views
gage and GO analysis
GO
convert
gage
GO
convert
gage
updated 10.3 years ago by
Reema Singh
▴ 570 • written 10.3 years ago by
Guest User
★ 13k
0
votes
0
replies
1.3k
views
Pathview with minor species
Microarray
Annotation
Bacillus subtilis
gage
pathview
Microarray
Annotation
gage
pathview
10.2 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
2.1k
views
Pathview with minor species
Microarray
Annotation
GO
Bacillus subtilis
gage
pathview
Microarray
Annotation
GO
gage
10.2 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
1.1k
views
Update in the gage RNA-seq pathway analysis joint workflow
limma
edgeR
gage
limma
edgeR
gage
10.2 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.4k
views
Can GAGE be used for transcript set pathway analysis
Pathways
gage
Pathways
gage
updated 10.0 years ago by
Luo Weijun
★ 1.6k • written 10.0 years ago by
sun
▴ 100
0
votes
1
reply
1.0k
views
GAGE Package: Problem with Affymetrix hg u133 plus 2 probeset IDs conversion to Gene names or vice versa
convert
gage
convert
gage
12.2 years ago
Javerjung Sandhu
▴ 200
50 results • Page
1 of 1
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Replies
Comment: Batch/method effect correction on a cohort of patients with RUVseq and DESeq2
by
Alexandre
• 0
My code for the sessionInfo() . If the pictures are too big, I will downsize them. THank you again for reading my post ! ```r > sessionInf…
Comment: Reproducibility issue with scran together with lapply and BiocParallel
by
ATpoint
★ 4.0k
Thanks Aaron for the response. RNGseed (for me) has no effect. I actually stumbled over this in one of my analysis where I have a constant …
Comment: Opposite sign of LFC in count plots of DEGs (DESeq2)
by
winwater0928
• 0
Thank you for your comment! 1)"Your contrast is comparing LGR5 to Homeostasis." means (Lgr5)/(Homeostasis). Is it right? Then, I think if…
Answer: Reproducibility issue with scran together with lapply and BiocParallel
by
Aaron Lun
★ 28k
IIRC **BiocParallel** switches to a different RNG when inside its own functions like `bplapply` - specifically L'Ecuyer-CMRG, as opposed to…
Comment: DESeq2 output used for PCA plot on R studio
by
swbarnes2
★ 1.3k
This looks terrible for RNASeq data, because it's not RNASeq data. It's a matrix of pretty random numbers, which you know because you poste…
Votes
C: null model and DEXSeqDataSet object in DEXSEQ
A: Are published RNA seq data analyses often wrong in calculating p-values and FDR?
A: How to explain how DESeq2 works to someone with zero bioinformatics background?
Answer: Interpret plot from DiffBind
Answer: How to retrieve gene ontology GO class from gene list?
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