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keggsoap
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834
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KEGGSOAP:: KEGGxmlns object not found
keggsoap
keggrest
6.0 years ago
doctor.dee005
• 0
1
vote
5
replies
2.0k
views
About the state of KEGG-related packages
KEGGSOAP
KEGGgraph
keggorthology
clusterProfiler
KEGGprofile
PathNet
KEGGSOAP
KEGGgraph
updated 10.8 years ago by
Luo Weijun
★ 1.6k • written 10.8 years ago by
enricoferrero
▴ 660
1
vote
16
replies
2.0k
views
error installing KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 11.3 years ago by
Martin Morgan
25k • written 11.3 years ago by
array chip
▴ 420
0
votes
0
replies
1.1k
views
KEGGREST package is available in devel
KEGGSOAP
KEGGREST
KEGGSOAP
KEGGREST
11.3 years ago
Dan Tenenbaum
★ 8.2k
0
votes
1
reply
830
views
Problem in KEGGSOAP package
KEGGSOAP
KEGGSOAP
updated 11.3 years ago by
Dan Tenenbaum
★ 8.2k • written 11.3 years ago by
Asta Laiho
▴ 120
0
votes
2
replies
1.0k
views
KEGGSOAP: list.pathways(org) or alternative way
Pathways
Organism
KEGGSOAP
Pathways
Organism
KEGGSOAP
updated 11.7 years ago by
Marc Carlson
★ 7.2k • written 11.7 years ago by
Jenny Kar
▴ 30
0
votes
5
replies
1.2k
views
KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 12.2 years ago by
Ricardo Silva
▴ 20 • written 12.2 years ago by
Ricardo Silva
▴ 110
0
votes
1
reply
1.2k
views
FrozenRMA how to
Microarray
Network
hgu133plus2
Biobase
PROcess
KEGGSOAP
beadarray
EBImage
edgeR
frma
updated 12.2 years ago by
Matthew McCall
▴ 830 • written 12.2 years ago by
Alex Sanchez
▴ 20
0
votes
0
replies
945
views
PostForm() with KEGG
GO
Cancer
KEGGSOAP
GO
Cancer
KEGGSOAP
12.2 years ago
Voke AO
▴ 760
0
votes
0
replies
961
views
Problem using KEGGSOAP: multiple genes per identity
Pathways
KEGGSOAP
Pathways
KEGGSOAP
12.3 years ago
January Weiner
▴ 240
0
votes
2
replies
1.4k
views
A bug in either KEGG or KEGGSOAP?
Pathways
KEGGSOAP
Pathways
KEGGSOAP
updated 12.3 years ago by
Marc Carlson
★ 7.2k • written 12.3 years ago by
Sang Chul Choi
▴ 230
0
votes
1
reply
797
views
KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 12.3 years ago by
Marc Carlson
★ 7.2k • written 12.3 years ago by
Ricardo Silva
▴ 110
0
votes
1
reply
1.1k
views
KEGGsoap: Space required after the Public Identifier
KEGGSOAP
KEGGSOAP
updated 12.3 years ago by
Martin Morgan
25k • written 12.3 years ago by
seth redmond
▴ 70
0
votes
1
reply
839
views
KEGGSOAP incomplete list.pathways
Pathways
KEGGSOAP
Pathways
KEGGSOAP
updated 12.5 years ago by
Marc Carlson
★ 7.2k • written 12.5 years ago by
Guest User
★ 13k
0
votes
2
replies
1.0k
views
Problem installing KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 12.5 years ago by
Dan Tenenbaum
★ 8.2k • written 12.5 years ago by
Paolo Sonego
▴ 140
0
votes
0
replies
814
views
SSOAP functions
KEGGSOAP
KEGGSOAP
13.0 years ago
Michael Gormley
▴ 60
0
votes
2
replies
3.3k
views
GEOquery -> cannot open URL 'ftp://ftp.ncbi.nih.gov/pub/geo/DATA/SeriesMatrix/ ....
KEGGSOAP
GEOquery
KEGGSOAP
GEOquery
updated 13.3 years ago by
Sean Davis
21k • written 13.3 years ago by
Manca Marco PATH
▴ 340
0
votes
1
reply
1.5k
views
KEGGSOAP, hgu95av2.db: limited functionality
Pathways
hgu95av2
probe
KEGGSOAP
Pathways
hgu95av2
probe
KEGGSOAP
updated 14.2 years ago by
Marc Carlson
★ 7.2k • written 14.2 years ago by
Ludwig Geistlinger
▴ 70
0
votes
2
replies
999
views
KEGGSOAP returning blank pages
Cancer
KEGGSOAP
Cancer
KEGGSOAP
updated 14.7 years ago by
Marc Carlson
★ 7.2k • written 14.7 years ago by
Daniel Brewer
★ 1.9k
0
votes
0
replies
963
views
KEGGSOAP package
KEGGSOAP
KEGGSOAP
14.7 years ago
Glazko, Galina
▴ 350
0
votes
0
replies
947
views
KEGGSOAP package: I can't retrieve KEGG pathway diagrams
hgu133a
KEGGSOAP
hgu133a
KEGGSOAP
14.8 years ago
Paolo Sonego
▴ 140
0
votes
3
replies
1.3k
views
KEGGSOAP: problem with get.pathways.by.genes()
Pathways
convert
KEGGSOAP
Pathways
convert
KEGGSOAP
updated 15.0 years ago by
Saroj K Mohapatra
▴ 400 • written 15.0 years ago by
Julien Meunier
▴ 30
0
votes
0
replies
776
views
KEGGSOAP install problem
Cancer
KEGGSOAP
Cancer
KEGGSOAP
15.0 years ago
Daniel Brewer
★ 1.9k
0
votes
4
replies
1.2k
views
KEGGSOAP problem
KEGGSOAP
KEGGSOAP
updated 15.0 years ago by
Vincent J. Carey, Jr.
6.7k • written 15.0 years ago by
Glazko, Galina
▴ 350
0
votes
2
replies
1.4k
views
KEGGSOAP (installation?) problem
KEGGSOAP
KEGGSOAP
updated 15.0 years ago by
Marc Carlson
★ 7.2k • written 15.0 years ago by
Paolo Sonego
▴ 140
0
votes
3
replies
1.4k
views
building enzyme centric metabolic network
Network
KEGGSOAP
Network
KEGGSOAP
updated 15.1 years ago by
Martin Morgan
25k • written 15.1 years ago by
anupam sinha
▴ 270
0
votes
3
replies
1.2k
views
Retrieving KEGG pathway diagrams via KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 15.1 years ago by
Paolo Sonego
▴ 140 • written 15.1 years ago by
Daren Tan
▴ 120
0
votes
0
replies
911
views
Visulising KEGG pathways using KEGGSOAP - example code
Pathways
geneplotter
KEGGSOAP
biomaRt
GEOquery
Pathways
geneplotter
KEGGSOAP
biomaRt
15.1 years ago
michael watson IAH-C
★ 3.4k
0
votes
1
reply
786
views
KEGG pathway IDs ,issing
Annotation
Cancer
KEGGSOAP
Annotation
Cancer
KEGGSOAP
updated 15.1 years ago by
Marc Carlson
★ 7.2k • written 15.1 years ago by
Daniel Brewer
★ 1.9k
0
votes
1
reply
1.0k
views
KEGGSOAP: color.pathway.by.objects
Pathways
KEGGSOAP
Pathways
KEGGSOAP
updated 16.7 years ago by
John Zhang
★ 2.9k • written 16.7 years ago by
Alexander C Cambon
▴ 30
0
votes
3
replies
926
views
libraries or commands to help with parsing or handling web based database queries
PROcess
KEGGSOAP
PROcess
KEGGSOAP
updated 17.2 years ago by
Thomas Girke
★ 1.7k • written 17.2 years ago by
ALAN SMITH
▴ 40
0
votes
7
replies
1.3k
views
KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 17.4 years ago by
Nianhua Li
▴ 870 • written 17.5 years ago by
Naomi Altman
★ 6.0k
0
votes
0
replies
793
views
KEGGSOAP Question: get.pathways.by.compounds
Pathways
KEGGSOAP
Pathways
KEGGSOAP
17.5 years ago
Nianhua Li
▴ 870
0
votes
0
replies
918
views
KEGGSOAP questions: how to handle multiple annotations in R data frames, and why does a "for" loop only use one annotation.
Annotation
KEGGSOAP
Annotation
KEGGSOAP
17.5 years ago
ALAN SMITH
▴ 40
0
votes
2
replies
1.1k
views
help with KEGG or KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 17.5 years ago by
Nianhua Li
▴ 870 • written 17.5 years ago by
ALAN SMITH
▴ 40
0
votes
0
replies
681
views
Inconsistent results returned from KEGG
KEGGSOAP
KEGGSOAP
18.1 years ago
michael watson IAH-C
★ 3.4k
0
votes
12
replies
2.1k
views
KEGGSOAP
KEGGSOAP
KEGGSOAP
updated 18.1 years ago by
Seth Falcon
★ 7.4k • written 18.1 years ago by
Dr.Mayhaus Manuel
▴ 30
0
votes
0
replies
917
views
problem with get.genes.by.pathway
Biobase
reposTools
KEGGSOAP
Biobase
reposTools
KEGGSOAP
18.6 years ago
Kimpel, Mark W
▴ 890
0
votes
1
reply
1.2k
views
Bioconductor Install Problems
Rgraphviz
KEGGSOAP
Rgraphviz
KEGGSOAP
updated 19.3 years ago by
Seth Falcon
★ 7.4k • written 19.3 years ago by
Smith, Troy NIH/NCI
▴ 10
0
votes
0
replies
645
views
mark.pathway.by.objects return NULL
KEGGSOAP
KEGGSOAP
19.3 years ago
Yi-Xiong Sean Zhou
▴ 50
0
votes
0
replies
1.0k
views
KEGGSOAP - Error in xmlName(node[[1]]) : no applicable method for "xmlName"
KEGGSOAP
KEGGSOAP
19.3 years ago
michael watson IAH-C
★ 3.4k
0
votes
2
replies
861
views
Problems installing KEGGSOAP
KEGGSOAP
KEGGSOAP
19.3 years ago
michael watson IAH-C
★ 3.4k
0
votes
2
replies
1.3k
views
pathway analysis package
RBGL
KEGGSOAP
RBGL
KEGGSOAP
updated 19.4 years ago by
Sean Davis
21k • written 19.4 years ago by
Josephine.Liang@uchsc.edu
▴ 60
43 results • Page
1 of 1
Recent ...
Replies
Comment: Cannot connect to ExperimentHub server
by
Jiayu
• 0
Many thanks and it also resolved the same issue for me!
Comment: Help with running egsea()
by
Chris
• 0
I tried egsea.ma and got this error: gsa = egsea.ma(numeric_matrix, vector_group, probe_annotation, contrasts = contrast_matrix, gs.an…
Comment: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
by
angelathuynh5
• 0
Thank you for your response. To clarify, the process of making a heatmap performs rowscaling so it takes the value - (mean/std). And to res…
Comment: Method to find pathways different between 2 groups
by
Gordon Smyth
50k
sigPathway is another method that does not account for inter-gene correlation and which gives inflated significance, as we showed in our 20…
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
by
James W. MacDonald
65k
I doubt you have that many contrasts. I think that is probably the number of rows. What does `dim(fit)` return (and `head(fit$coef)`)?
Votes
Answer: Cannot connect to ExperimentHub server
Answer: confused with tximport counts abundance using salmon input
Answer: Getting Error in hclust(d, method = method): NA/NaN/Inf in foreign function call
Answer: error in limma , contrast.matrix Number of rows of contrast matrix must match nu
Answer: Extremely small p-values using Limma for proteomic data
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42k
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