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pathview
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0
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2
replies
4.9k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 4.0 years ago by
Helen
• 0 • written 8.0 years ago by
tarun2
• 0
0
votes
0
replies
1.7k
views
pathview and gage server connection issue
pathview
gage
pathway analysis
kegg
visualization
8.0 years ago
Luo Weijun
★ 1.6k
1
vote
1
reply
2.0k
views
Highlight ECs by KEGG module
pathview
KEGG
updated 8.3 years ago by
Luo Weijun
★ 1.6k • written 8.3 years ago by
wrodriguez
• 0
0
votes
0
replies
1.4k
views
Pathview: cannot save pathway "01100"
pathview
8.3 years ago
fansili2013
▴ 50
1
vote
2
replies
3.1k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview
KEGG
parsing
8.3 years ago
ladypurrsia
▴ 10
1
vote
3
replies
3.1k
views
Pathview pathview kegg.native=TRUE throws error in img
pathview
kegg
error
bioconductor
rnaseq
updated 8.3 years ago by
map2085
▴ 40 • written 9.0 years ago by
guillermo.marco
▴ 30
0
votes
0
replies
1.6k
views
Custom graphNEL object for pathview
pathview
mirintegrator
miRNA
8.4 years ago
drowsygoat
▴ 30
1
vote
2
replies
3.2k
views
Using GAGE to Analyze Pathway Enrichment Directly from Fold Change Data
GAGE
Gene Ontology
rna-seq
pathview
updated 8.4 years ago by
Luo Weijun
★ 1.6k • written 8.4 years ago by
JMallory
• 0
0
votes
3
replies
3.2k
views
Pathview -- Error in korg[ridx, coln] : subscript out of bounds
pathview
korg
subscript out of bounds
Tutorial
updated 8.4 years ago by
Luo Weijun
★ 1.6k • written 8.4 years ago by
aacevedo
• 0
2
votes
11
replies
6.2k
views
Recent build and parsing error in pathview
pathview
KEGGgraph
gage
pathway
pathway analysis
8.6 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
1.7k
views
Multiple samples on the same graph
Pathview
probe
updated 8.6 years ago by
Luo Weijun
★ 1.6k • written 8.6 years ago by
Luiz
• 0
0
votes
0
replies
1.1k
views
Get bugs from pathview package
pathview
8.7 years ago
joseph
▴ 50
0
votes
7
replies
3.5k
views
Error in pathview - came out of nowhere without any source code modification
pathview
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
Mataivic
• 0
0
votes
2
replies
2.0k
views
ID unmatched in pathview
pathview
updated 8.8 years ago by
Mataivic
• 0 • written 8.8 years ago by
joseph
▴ 50
0
votes
0
replies
2.0k
views
News:
Pathview Web server published in NAR
pathway analysis
visualization
data integration
omics
pathview
News
8.8 years ago
Luo Weijun
★ 1.6k
0
votes
1
reply
2.8k
views
error when rendering pathway with pathview package
pathview
updated 8.8 years ago by
Luo Weijun
★ 1.6k • written 8.8 years ago by
holgerbrandl
▴ 10
0
votes
0
replies
1.3k
views
How to pathway analysis of Arabidopsis thaliana organism
microarray
pathview
9.0 years ago
avinash gupta
▴ 130
0
votes
0
replies
1.7k
views
GAGE from DESeq: pairwise comparison between 1 reference and 3 samples
gage
deseq
pathview
9.0 years ago
user31888
▴ 30
0
votes
14
replies
6.6k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub
AnnotationDbi
AnnotationForge
pathview
9.1 years ago • updated 3.5 years ago
Jenny Drnevich
★ 2.0k
0
votes
4
replies
2.8k
views
Error: Pathway analysis using Sleuth results
pathview
gage
rna-seq
R
sleuth
9.1 years ago
bioinf
▴ 10
0
votes
2
replies
2.4k
views
Questions about Pathview, maybe also gage
Pathview
Gage
R
updated 9.2 years ago by
bioinf
▴ 10 • written 9.6 years ago by
ChIP-Tease
• 0
0
votes
2
replies
2.1k
views
GAGE and Pathview from RNA-Seq: 'ref.idx' and 'samp.idx' when no replicates
GAGE
pathview
updated 9.2 years ago by
Luo Weijun
★ 1.6k • written 9.2 years ago by
user31888
▴ 30
1
vote
2
replies
2.6k
views
can KEGG figures produced by pathview be used in publication, or that they are copyrighted ?
pathview
clusterprofiler
9.4 years ago
assaf www
▴ 140
4
votes
3
replies
3.2k
views
Pathview: Exporting non native KEGG pathway to PNG
pathview
bioconductor
graphics
graphviz
Pathview
updated 9.4 years ago by
dondelelcaro
▴ 10 • written 9.5 years ago by
guillermo.marco
▴ 30
1
vote
0
replies
1.1k
views
pathview should support not creating new devices
pathview
9.4 years ago
dondelelcaro
▴ 10
1
vote
1
reply
3.5k
views
Pathview color code and gene homolog handling?
pathview
updated 9.4 years ago by
Luo Weijun
★ 1.6k • written 9.5 years ago by
devang3110
• 0
1
vote
1
reply
2.4k
views
Pathview & topGO
R
GO
topGO
pathview
updated 9.5 years ago by
Luo Weijun
★ 1.6k • written 9.5 years ago by
cabezasdelafuented
▴ 10
0
votes
2
replies
2.0k
views
Pathview: Exporting non native KEGG pathway ignoring same.layer argument
Pathview
rgraphviz
graphviz
KEGG
updated 9.5 years ago by
Luo Weijun
★ 1.6k • written 9.5 years ago by
guillermo.marco
▴ 30
0
votes
0
replies
1.8k
views
Using Pathview with gene.idtype = "SYMBOL"
Pathview
symbol
9.5 years ago
sofia.figueiredo
▴ 10
1
vote
2
replies
2.0k
views
Need to convert gene IDs for GAGE pathway analysis of honey bee RNA-seq data
R
gage package
rnaseq
pathview
9.5 years ago
joanito.liberti
• 0
8
votes
13
replies
13k
views
Pathview: *** caught segfault *** cause 'memory not mapped'
pathview
segfault
updated 9.6 years ago by
redpick13
▴ 40 • written 10.2 years ago by
user31888
▴ 30
1
vote
1
reply
2.4k
views
Using pathview with uncommon species leads to Errors
pathview
Kegg
rnaseq
data visualization
updated 9.6 years ago by
Luo Weijun
★ 1.6k • written 9.6 years ago by
rafre
• 0
2
votes
2
replies
3.9k
views
Why Pathview shows just red color (up-regulated genes) on a pathway?
Pathview
pathway analysis
differential gene expression
updated 9.7 years ago by
Luo Weijun
★ 1.6k • written 9.7 years ago by
Sara
▴ 20
0
votes
6
replies
5.0k
views
Error in using Pathview package. Do not print the pathways provided by GAGE analysis
gage
pathview
error
updated 9.7 years ago by
Luo Weijun
★ 1.6k • written 9.8 years ago by
marie.bordone
• 0
1
vote
2
replies
2.8k
views
Please help with pathway analysis using Pathview
pathview
pathway analysis
updated 9.7 years ago by
Luo Weijun
★ 1.6k • written 9.7 years ago by
Sara
▴ 20
0
votes
1
reply
2.6k
views
Pathview: visualization of data
pathview
data visualization
updated 10.0 years ago by
Luo Weijun
★ 1.6k • written 10.0 years ago by
Guido Hooiveld
★ 4.1k
0
votes
1
reply
1.6k
views
Using Gage and pathview with previously processed data
pathview
gage
r
kegg
rnaseq
updated 10.0 years ago by
Luo Weijun
★ 1.6k • written 10.0 years ago by
bsguida
• 0
1
vote
3
replies
2.3k
views
Discrepancy in gene set size between gage() and geneData()
gage
gene set analysis
pathview
kegg
pathway analysis
10.0 years ago
serpalma.v
▴ 60
0
votes
1
reply
1.8k
views
How to perform pathway analysis of Candida albicans using pathview?
pathview
updated 10.1 years ago by
Luo Weijun
★ 1.6k • written 10.1 years ago by
daniel.molecular
• 0
0
votes
0
replies
2.1k
views
Pathview Web Server: user friendly pathway visualization and data integration
pathview
pathway analysis
visualization
web server
omics data
10.1 years ago
Weijun Luo
• 0
2
votes
3
replies
6.1k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 4.6 years ago by
najib
• 0 • written 10.2 years ago by
Dani
▴ 20
1
vote
1
reply
1.7k
views
embed url in pathview images
pathview
r
pdf
kegg
graphviz
updated 10.2 years ago by
Luo Weijun
★ 1.6k • written 10.2 years ago by
firstdayonthejob2003
• 0
3
votes
5
replies
3.4k
views
Explanation of warning output of pathview regarding visualization of a KEGG pathway with Graphviz format
pathview
clusterProfiler
KEGGpath
visualization
Graphviz
updated 10.3 years ago by
Luo Weijun
★ 1.6k • written 10.3 years ago by
svlachavas
▴ 840
0
votes
1
reply
3.0k
views
Input file of NGS data for Pathview
rnaseq
pathview
data visualization
updated 10.3 years ago by
Luo Weijun
★ 1.6k • written 10.3 years ago by
amoltej
▴ 10
0
votes
5
replies
3.8k
views
Gene Symbol with Pathview
pathview
bioconductor
kegg
visualization
updated 10.4 years ago by
Luo Weijun
★ 1.6k • written 10.4 years ago by
abhinavbn
• 0
0
votes
3
replies
2.3k
views
Using pathview() with custom graphNEL objects
pathview
mirintegrator
10.4 years ago
prosomething
• 0
0
votes
4
replies
3.2k
views
GAGE kegg.gsets function does not work: 'names' attribute [1] must be the same length as the vector [0]
gage
pathview
10.4 years ago
martin.hoelzer
▴ 20
2
votes
6
replies
4.2k
views
Fixing download.kegg, from pathview(), which returns empty xml
pathview
download.kegg()
xml
updated 10.5 years ago by
Luo Weijun
★ 1.6k • written 10.5 years ago by
lucmoitinho
• 0
2
votes
2
replies
2.3k
views
Output from pathview does not seem to match input
pathview
gage
pathway analysis
updated 10.6 years ago by
Luo Weijun
★ 1.6k • written 10.6 years ago by
bdp
• 0
0
votes
1
reply
1.8k
views
GAGE/Pathview now support 3000 KEGG species and 19 GO species (with BioC 2.14)
GO
gage
pathview
GO
gage
pathview
updated 10.7 years ago by
jackipchiho
▴ 10 • written 11.7 years ago by
Luo Weijun
★ 1.6k
146 results • Page
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Comment: Question on processing compound protein groups in limpa
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JKim
• 0
Many thanks. I appreciate your advice.
Answer: Question on processing compound protein groups in limpa
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53k
Different people have different ways of dealing with compound protein groups. You could just leave them in the analysis, in which case limp…
Answer: Correct usage of limpa for protein input
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limpa can work on protein-level quantifications, but they must be intensity-based and must be on the log scale. From what I read (<https://…
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Answer: Question on processing compound protein groups in limpa
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