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Showing :
pathview
•
reset
0
votes
0
replies
29
views
pathview error "negative length vectors are not allowed
pathview
kegg
KEGG
2 days ago
Mauricio Diego
• 0
0
votes
0
replies
145
views
SSL connect error in e.g. pathview from R version 4 in Windows 10
pathview
SSL
curl
9 weeks ago
Matthias
• 0
1
vote
4
replies
482
views
pathview - a species in KEGG pathway but not in 'korg'
pathview
KEGG
Oryza_sativa
3 months ago
Jiyoung Lee
• 0
1
vote
1
reply
469
views
Error with Pathview: Bad Request (HTTP 400)
KEGGREST
pathview
R
updated 5 months ago by
Guido Hooiveld
★ 3.7k • written 5 months ago by
morgan.sobol
• 0
0
votes
2
replies
651
views
pathview: Warning: Failed to download KEGG xml/png files, hsa04110 skipped!
pathview
5 months ago
덕윤
• 0
4
votes
3
replies
2.8k
views
only 0's may be mixed with negative subscripts
pathview
updated 6 months ago by
saadatabu1996
▴ 10 • written 6.8 years ago by
nature.hunger
▴ 30
1
vote
3
replies
678
views
Many NAs using TAIR IDs for plotting KEGG pathways using pathview
KEGG
TAIR_IDs
KEGGdzPathwaysGEO
pathview
updated 9 months ago by
James W. MacDonald
63k • written 9 months ago by
Arctic
• 0
4
votes
6
replies
2.4k
views
Pathview unable to download pathways
clusterProfiler
KEGGgraph
clusterpr
KEGG
pathview
updated 12 months ago by
Guido Hooiveld
★ 3.7k • written 15 months ago by
rama
▴ 10
3
votes
13
replies
1.7k
views
pathview says my nonmodel species is unknown: "species invalid"
KEGGREST
KEGG
gage
pathview
13 months ago • updated 7 months ago
nute11a
▴ 10
0
votes
1
reply
525
views
Pathview error Warning: Parsing ./mmu04928.xml file failed, please check the file!
KEGGgraph
pathview
updated 15 months ago by
Guido Hooiveld
★ 3.7k • written 15 months ago by
k.jane.olczak
• 0
0
votes
1
reply
800
views
Help with Pathview: No annotation package for a species, gene symbols not mapped!
annotation_package
not_available_in_BioConductor
pathview
updated 11 months ago by
Rocio
• 0 • written 19 months ago by
bertranbio
• 0
2
votes
2
replies
707
views
pathview returns incorrect mappings for yeast
org.Sc.sgd.db
org.Sc
pathview
20 months ago
chase.mateusiak
• 0
0
votes
3
replies
755
views
pathview: unable to use option "out.suffix"
pathview
updated 2.2 years ago by
Luo Weijun
★ 1.6k • written 2.2 years ago by
文祥
• 0
0
votes
2
replies
1.3k
views
Drawing custom KEGG pathways
pathview
KEGG
2.3 years ago
curiousmind007
▴ 10
1
vote
2
replies
646
views
Pathview won't render some KEGG pathways
pathview
2.4 years ago
Duncan
• 0
1
vote
2
replies
1.1k
views
PATHVIEW incorrect values being plotted in output
pathview
org.Hs.eg.db
2.4 years ago
Rodrigo
• 0
44
votes
29
replies
9.6k
views
.onLoad failed in loadNamespace() for 'org.Hs.eg.db'
org.Hs.eg.db
pathview
updated 2.4 years ago by
Kevin Ushey
▴ 130 • written 2.4 years ago by
Arun
▴ 160
0
votes
1
reply
702
views
News:
SBGNview manuscript on bioRxiv now
pathway
SBGNview
Reactome
pathview
PANTHER
written 2.5 years ago by
Luo Weijun
★ 1.6k
0
votes
0
replies
716
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
singlecellRNA-Seq
pathview
statistics
R
2.5 years ago • updated 2.4 years ago
Luo Weijun
★ 1.6k
6
votes
5
replies
1.2k
views
KEGG analysis for plasmodium
KEGG
gage
gageData
pathview
updated 2.5 years ago by
Luo Weijun
★ 1.6k • written 2.5 years ago by
MOHAMMAD
• 0
1
vote
1
reply
876
views
News:
SBGNview: Data Analysis, Integration and Visualization on 5000+ Pathways/3000+ Species
SBGNview
pathways
SBGNview.data
pathview
visualization
2.6 years ago • updated 2.5 years ago
Luo Weijun
★ 1.6k
1
vote
2
replies
908
views
Can I create a gene set using GAGE?
gage
pathview
gageData
written 2.7 years ago by
Emilia
▴ 30
0
votes
1
reply
584
views
Change colors pathview
pathview
updated 2.8 years ago by
Luo Weijun
★ 1.6k • written 2.8 years ago by
da.de
▴ 20
0
votes
0
replies
699
views
Job:
Biostatistics/Bioinformatics Research Scientist at UNC Charlotte
R
statistics
pathview
singlecellRNA-Seq
2.8 years ago • updated 2.5 years ago
Luo Weijun
★ 1.6k
0
votes
0
replies
887
views
Pathview: empty metabolic map
pathview
2.9 years ago
landenshanie
▴ 40
0
votes
2
replies
915
views
Hightlight genes/metabolites in Pathview and ReactomePA
pathview
ReactomePA
updated 3.2 years ago by
James W. MacDonald
63k • written 3.2 years ago by
emisecherre
• 0
0
votes
0
replies
430
views
Pathview colors only matching ids?
pathview
3.2 years ago
okna0215
▴ 10
1
vote
0
replies
671
views
Pathview : why are some genes not colored?
pathview
rna-seq
3.2 years ago
okna0215
▴ 10
0
votes
1
reply
604
views
Argument map.symbol converting IDs even when its value is FALSE
pathview
updated 3.3 years ago by
Kevin Blighe
3.8k • written 4.5 years ago by
arthur.vinx
• 0
0
votes
1
reply
511
views
Multiple samples in pathview with different colors
pathview
multiple samples
updated 2.3 years ago by
esteban.peguero
• 0 • written 3.6 years ago by
mshofner
• 0
0
votes
0
replies
641
views
gage function problem in R
gage
R
kegg
pathview
updated 3.6 years ago by
Michael Love
40k • written 3.6 years ago by
eozcan
• 0
4
votes
4
replies
1.2k
views
How I interpret this plot from pathview
pathview
kegg
r
pathway
3.9 years ago • updated 3.8 years ago
AZ
▴ 30
0
votes
0
replies
766
views
KEGG pathway analysis using gage/pathview non KEGG organism duplicate K IDs
gage
pathview
KEGG
Gene enrichment analysis
3.9 years ago
MimR
• 0
0
votes
3
replies
895
views
None of the genes or compounds mapped to the pathway!
pathview
AnnotationDbi
updated 4.0 years ago by
Michael Love
40k • written 4.0 years ago by
kevinvdburg
• 0
0
votes
0
replies
793
views
Modifying a Pathview function which needs an internet connection so that it can work without an internet connection.
Pathview
Gene Mapping
KEGG
4.0 years ago
omarrafiqued
▴ 50
0
votes
0
replies
524
views
pathview : kegg gene ID in the visualisation ?
pathview
4.1 years ago
cedric.vmdl
• 0
0
votes
2
replies
926
views
Issue with xml files downloaded with `pathview()`
pathview
kegg
xml
updated 4.2 years ago by
Luo Weijun
★ 1.6k • written 4.2 years ago by
anamaria
▴ 10
0
votes
2
replies
1.4k
views
pathview: object 'bods' not found
pathview
updated 4.2 years ago by
anamaria
▴ 10 • written 5.0 years ago by
Shi-Xiang Wang
• 0
0
votes
1
reply
600
views
Pathview won't colour even with matching IDs
pathview
4.5 years ago
francesco.gualdrini
• 0
0
votes
0
replies
628
views
Help with mapping Kegg hsa01100 using pathview
kegg
pathway
pathview
4.5 years ago
Ahdee
▴ 50
0
votes
0
replies
768
views
Pathview input error: non-numeric variable in data frame
pathview
kegg
pathways
package
5.0 years ago
anc.informatics
• 0
1
vote
5
replies
2.5k
views
KEGG enrichment for non-model
kegg
pathway analysis
non-model
gage
pathview
updated 2.2 years ago by
najib
• 0 • written 5.2 years ago by
bekah
▴ 20
0
votes
4
replies
2.3k
views
pathview: Warning: Download of hsa04110 xml and png files failed!
pathview
5.2 years ago
masamiwata
• 0
1
vote
4
replies
1.3k
views
Pathview error: ran fine yesterday
pathview
updated 5.3 years ago by
Martin Morgan
25k • written 6.3 years ago by
Epic Tinus
▴ 10
0
votes
1
reply
1.3k
views
Pathview results interpretation
pathview
interpretation
5.3 years ago
Aurora
▴ 20
0
votes
2
replies
3.3k
views
Cannot open URL 'http://rest.kegg.jp/get/osaNA/kgml': HTTP status was '400 Bad Request'
gage
gage package
pathview
rna-seq
updated 18 months ago by
Helen
• 0 • written 5.6 years ago by
tarun2
• 0
0
votes
0
replies
1.0k
views
pathview and gage server connection issue
pathview
gage
pathway analysis
kegg
visualization
5.6 years ago
Luo Weijun
★ 1.6k
1
vote
1
reply
1.2k
views
Highlight ECs by KEGG module
pathview
KEGG
updated 5.8 years ago by
Luo Weijun
★ 1.6k • written 5.9 years ago by
wrodriguez
• 0
0
votes
0
replies
883
views
Pathview: cannot save pathway "01100"
pathview
5.9 years ago
fansili2013
▴ 50
1
vote
2
replies
2.1k
views
Error in Pathview parsing: "Parsing ./ko00195.xml file failed, please check the file!"
pathview
KEGG
parsing
5.9 years ago
ladypurrsia
▴ 10
50 results • Page
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Comment: DMRcate design
by
James W. MacDonald
63k
That's what identical context means.
Comment: DMRcate design
by
Jitendra
▴ 10
Thanks James, but I did not understand it clearly. Could I used same Limma design matrix for DMRcate?
Comment: Steps needed to change design (relevel factors) in DESeq2
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jd774
• 0
Thanks for the example code, would the `"condition_1_vs_2"` and `"condition_2_vs_1"` giving same or different results on DEGs and normalize…
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63k
You might want to filter first though. ``` fun <- function(deseqobj, contvec, cutoff) { lildds <- dds[rowMeans(assays(deseqobj…
Votes
Bioconductor 3.18 db0s, OrgDbs, and TxDbs now available
Comment: Timely differentially expressed genes
Comment: NPARC package y-variable
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