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pathview
•
reset
0
votes
0
replies
28
views
GAGE results interpretation with gene-foldchange as input for cases of all-negative foldchange
GO
KEGG
gage
pathview
1 day ago
danalvoronov
▴ 10
0
votes
1
reply
203
views
Help with identifying genes mapped to KEGG pathway using pathview
pathview
updated 7 weeks ago by
Guido Hooiveld
★ 4.0k • written 8 weeks ago by
Julie
• 0
0
votes
3
replies
1.2k
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
updated 7 months ago by
Benji Bromberg
▴ 20 • written 8 months ago by
Mauricio Diego
• 0
0
votes
1
reply
1.5k
views
Doubts regarding Pathview
Annotation
pathview
Annotation
pathview
written 9.8 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
556
views
SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview
SSL
curl
10 months ago
Matthias
• 0
1
vote
4
replies
1.1k
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
11 months ago
Jiyoung Lee
• 0
1
vote
1
reply
1.3k
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 13 months ago by
Guido Hooiveld
★ 4.0k • written 13 months ago by
morgan.sobol
• 0
0
votes
2
replies
1.3k
views
pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
pathview
13 months ago
덕윤
• 0
4
votes
3
replies
3.2k
views
only 0's may be mixed with negative subscripts
pathview
updated 14 months ago by
saadatabu1996
▴ 10 • written 7.4 years ago by
nature.hunger
▴ 30
3
votes
13
replies
2.6k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
21 months ago • updated 15 months ago
nute11a
▴ 10
1
vote
3
replies
1.2k
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 17 months ago by
James W. MacDonald
65k • written 17 months ago by
Arctic
• 0
0
votes
1
reply
1.2k
views
Help with Pathview: No annotation package for a species, gene symbols not mapped!
annotation_package
not_available_in_BioConductor
pathview
updated 19 months ago by
Rocio
• 0 • written 2.2 years ago by
bertranbio
• 0
4
votes
6
replies
3.7k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 20 months ago by
Guido Hooiveld
★ 4.0k • written 23 months ago by
rama
▴ 10
0
votes
14
replies
4.8k
views
Easy way to turn OrgDb object from AnnotationHub into package?
AnnotationHub
AnnotationDbi
AnnotationForge
pathview
7.3 years ago • updated 21 months ago
Jenny Drnevich
★ 2.0k
0
votes
1
reply
807
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 23 months ago by
Guido Hooiveld
★ 4.0k • written 23 months ago by
k.jane.olczak
• 0
0
votes
2
replies
3.7k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 2.2 years ago by
Helen
• 0 • written 6.2 years ago by
tarun2
• 0
2
votes
2
replies
1.0k
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db
org.Sc
pathview
2.3 years ago
chase.mateusiak
• 0
2
votes
3
replies
4.9k
views
Pathview None of the genes or compounds mapped to the pathway
pathview
pathways
KEGG
empty map
updated 2.8 years ago by
najib
• 0 • written 8.4 years ago by
Dani
▴ 20
1
vote
5
replies
3.0k
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
0
votes
3
replies
1.1k
views
pathview: unable to use option "out.suffix"
pathview
updated 2.9 years ago by
Luo Weijun
★ 1.6k • written 2.9 years ago by
文祥
• 0
0
votes
1
reply
717
views
Multiple samples in pathview with different colors
pathview
multiple samples
updated 2.9 years ago by
esteban.peguero
• 0 • written 4.3 years ago by
mshofner
• 0
0
votes
2
replies
1.8k
views
Drawing custom KEGG pathways
pathview
KEGG
3.0 years ago
curiousmind007
▴ 10
1
vote
2
replies
835
views
Pathview won't render some KEGG pathways
pathview
3.0 years ago
Duncan
• 0
0
votes
0
replies
930
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq
pathview
statistics
R
3.1 years ago • updated 3.0 years ago
Luo Weijun
★ 1.6k
1
vote
2
replies
1.5k
views
PATHVIEW incorrect values being plotted in output
pathview
org.Hs.eg.db
3.1 years ago • updated 3.0 years ago
Rodrigo
• 0
44
votes
29
replies
11k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 3.1 years ago by
Kevin Ushey
▴ 130 • written 3.1 years ago by
Arun
▴ 160
0
votes
1
reply
941
views
News:
SBGNview manuscript on bioRxiv now
pathway
SBGNview
Reactome
pathview
PANTHER
written 3.1 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
931
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R
statistics
pathview
singlecellRNA-Seq
3.5 years ago • updated 3.1 years ago
Luo Weijun
★ 1.6k
6
votes
5
replies
1.6k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 3.2 years ago by
Luo Weijun
★ 1.6k • written 3.2 years ago by
MOHAMMAD
• 0
1
vote
1
reply
1.1k
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
3.2 years ago
Luo Weijun
★ 1.6k
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
0
votes
1
reply
832
views
Change colors pathview
pathview
updated 3.4 years ago by
Luo Weijun
★ 1.6k • written 3.4 years ago by
da.de
▴ 30
0
votes
0
replies
1.1k
views
Pathview: empty metabolic map
pathview
3.6 years ago
landenshanie
▴ 40
0
votes
2
replies
1.2k
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 3.9 years ago by
James W. MacDonald
65k • written 3.9 years ago by
emisecherre
• 0
0
votes
0
replies
611
views
Pathview colors only matching ids?
pathview
3.9 years ago
okna0215
▴ 10
1
vote
0
replies
937
views
Pathview : why are some genes not colored?
pathview
rna-seq
3.9 years ago
okna0215
▴ 10
0
votes
1
reply
789
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 4.0 years ago by
Kevin Blighe
★ 3.9k • written 5.2 years ago by
arthur.vinx
• 0
0
votes
0
replies
895
views
gage function problem in R
gage
R
kegg
pathview
updated 4.3 years ago by
Michael Love
42k • written 4.3 years ago by
eozcan
• 0
4
votes
4
replies
1.8k
views
How I interpret this plot from pathview
pathview
kegg
r
pathway
4.5 years ago
AZ
▴ 30
0
votes
0
replies
966
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage
pathview
KEGG
Gene enrichment analysis
4.6 years ago
MimR
• 0
0
votes
3
replies
1.3k
views
None of the genes or compounds mapped to the pathway!
pathview
AnnotationDbi
updated 4.6 years ago by
Michael Love
42k • written 4.6 years ago by
kevinvdburg
• 0
0
votes
0
replies
982
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview
Gene Mapping
KEGG
4.7 years ago
omarrafiqued
▴ 50
0
votes
0
replies
706
views
pathview : kegg gene ID in the visualisation ?
pathview
4.8 years ago
cedric.vmdl
• 0
0
votes
2
replies
1.2k
views
Issue with xml files downloaded with `pathview()`
pathview
kegg
xml
updated 4.8 years ago by
Luo Weijun
★ 1.6k • written 4.8 years ago by
anamaria
▴ 10
0
votes
2
replies
1.8k
views
pathview: object 'bods' not found
pathview
updated 4.8 years ago by
anamaria
▴ 10 • written 5.7 years ago by
Shi-Xiang Wang
• 0
0
votes
1
reply
826
views
Pathview won't colour even with matching IDs
pathview
5.2 years ago
francesco.gualdrini
• 0
0
votes
0
replies
785
views
Help with mapping Kegg hsa01100 using pathview
kegg
pathway
pathview
5.2 years ago
Ahdee
▴ 50
0
votes
0
replies
972
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
5.6 years ago
anc.informatics
• 0
0
votes
4
replies
2.7k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
5.9 years ago
masamiwata
• 0
1
vote
4
replies
1.6k
views
Pathview error: ran fine yesterday
pathview
updated 6.0 years ago by
Martin Morgan
25k • written 6.9 years ago by
Epic Tinus
▴ 10
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Comment: Error while installing BiocManager::install("org.Vdahliae.eg.db")
by
Patadù
▴ 10
Hi @marcelramos Thanks for the clarification. Yes, I have installed `org.Vdahlaie.eg.db` using the code you and Guido suggested and now i…
Comment: European Bioconductor Conference 2023 planning
by
angelaesper43
• 0
@Maria Doyle[sexdolltech][1]Hosting EuroBioC provides an excellent opportunity to showcase Bioconductor and computational biology research …
Comment: Ensembl plants at annotationHub?
by
Johannes Rainer
★ 2.0k
Dear Daniele, for which Ensembl release would you need the data? the most recent is 112, but if you used a different version before it wou…
Comment: Ensembl plants at annotationHub?
by
Daniele
• 0
Dear Johannes, Would it be possible to create the EnsDb for Triticum aestivum (IWGSC)? Thank you very much, Daniele
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
by
BioinfGuru
▴ 30
Figured it out with ?eigencorplot, thanks Michael. I was trying to pass 10 PCs when I only had 8, and I was including metadata columns that…
Votes
Answer: Error while installing BiocManager::install("org.Vdahliae.eg.db")
Comment: How can I create a eigencorplot of pca created from deseq2 object with PCAtools
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Answer: Importing a GraphNEL into Cytoscape with RCy3 with error: "Error in cyrestPUT(pa
Rsubread counting peaks ATACseq
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